bluuebunny/crossref_metadata_2025 huggingface dataset:
Simple derivations of the Hamilton–Jacobi equation and the eikonal equation without the use of canonical transformations
Authors: Small Alex , Lam Kai S.
Published: May 2011

The Hamilton–Jacobi equation in classical mechanics and the related eikonal equation in geometrical optics are often described as the “point of closest approach” between classical and quantum mechanics. Most textbook treatments of Hamilton–Jacobi theory are aimed at graduate students and derive the equation only after a long introduction to canonical transformations. Most treatments of the eikonal equation only emphasize its use in geometrical optics. We show that both the Hamilton–Jacobi equation and the eikonal equation can be derived by a common procedure using only elementary aspects of the Lagrangian and Hamiltonian formalisms introduced in undergraduate classical mechanics courses. Through this common approach, we hope to highlight to undergraduates the deep connections between classical mechanics, classical wave theory, and Schrödinger’s wave mechanics.
Corked bats, juiced balls, and humidors: The physics of cheating in baseball
Authors: Nathan Alan M. , Smith Lloyd V. , Faber Warren L. , Russell Daniel A.
Published: May 2011

Three questions of relevance to Major League Baseball are investigated from a physics perspective. Can a baseball be hit farther with a corked bat? Is there evidence that the baseball is more lively today than in earlier years? Can storing baseballs in a temperature- or humidity-controlled environment significantly affect home run production? These questions are subjected to a physics analysis, including an experiment and an interpretation of the data. The answers to the three questions are no, no, and yes, respectively.
Demonstration and study of the dispersion of water waves with a computer-controlled ripple tank
Authors: Ströbel Bernhard
Published: May 2011

The design of a ripple tank built in an undergraduate student project is described. Water waves are excited acoustically using computer programmable wave shapes. The projected wave patterns are recorded with a video camera and analyzed quantitatively. From the propagation of wave packets in distilled water at three different depths, the phase and group velocities are measured in the frequency range from 2 to 50 Hz. Good agreement with theory is found. The propagation of wave trains of different shapes is recorded and explained on the basis of the stationary phase approximation. Various types of precursors are detected. For a depth slightly above the critical depth and thus nearly dispersion-free, the solitary-like propagation of a single pulse is observed. In shallow water, the compression of a chirped pulse is demonstrated. Circular waves produced by falling water drops are recorded and analyzed.
More about Bohm’s quantum
Authors: Bernstein Jeremy
Published: May 2011

I give a pedagogical introduction to Bohm’s interpretation of quantum theory, suitable for graduate students.
Schwarzschild and de Sitter solutions from the argument by Lenz and Sommerfeld
Authors: Cuzinatto R. R. , Pimentel B. M. , Pompeia P. J.
Published: May 2011

The Lenz–Sommerfeld argument allows an ingenious and simple derivation of the Schwarzschild solution of Einstein equations of general relativity. We use the same reasoning to construct the de Sitter line element.
Two and three slit electron interference and diffraction experiments
Authors: Frabboni Stefano , Frigeri Cesare , Gazzadi Gian Carlo , Pozzi Giulio
Published: May 2011

Current nanotechnology techniques make possible the preparation of slits in the submicrometer range so that electron interference and diffraction experiments can be done even with a conventional electron microscope. If the instrument is also equipped with a field emission source, it is possible to follow almost in real time the transition from the image of the slits to their Fraunhofer pattern through the intermediate Fresnel diffraction images. We discuss our results for the two-slit experiment and illustrate them for the three-slit case.
Crystal Structure of the Maltose Transporter in a Pretranslocation Intermediate State
Authors: Oldham Michael L. , Chen Jue
Published: May 2011

An intermediate structure provides insight into how a transport substrate allosterically activates adenosine triphosphatase activity.
Carbon-Based Supercapacitors Produced by Activation of Graphene
Authors: Zhu Yanwu , Murali Shanthi , Stoller Meryl D. , Ganesh K. J. , Cai Weiwei , Ferreira Paulo J. , Pirkle Adam , Wallace Robert M. , Cychosz Katie A. , Thommes Matthias , Su Dong , Stach Eric A. , Ruoff Rodney S.
Published: May 2011

Activated microwave-exfoliated graphite oxide combined with an ionic liquid can be used to make an enhanced capacitor.
Evidence of a Global Magma Ocean in Io’s Interior
Authors: Khurana Krishan K. , Jia Xianzhe , Kivelson Margaret G. , Nimmo Francis , Schubert Gerald , Russell Christopher T.
Published: May 2011

Magnetic field measurements made near Jupiter’s moon Io strengthen the evidence for a magma ocean in its interior.
Disorder-Enhanced Transport in Photonic Quasicrystals
Authors: Levi Liad , Rechtsman Mikael , Freedman Barak , Schwartz Tal , Manela Ofer , Segev Mordechai
Published: May 2011

Optical interference in a photorefractive crystal is used to study light propagation in a controlled disordered system.
Local Macrophage Proliferation, Rather than Recruitment from the Blood, Is a Signature of T
H
2 Inflammation
Authors: Jenkins Stephen J. , Ruckerl Dominik , Cook Peter C. , Jones Lucy H. , Finkelman Fred D. , van Rooijen Nico , MacDonald Andrew S. , Allen Judith E.
Published: May 2011

Proliferation in situ, rather than immune cell recruitment, drives macrophage expansion in response to parasitic infection.
Application of a Broad-Range Resequencing Array for Detection of Pathogens in Desert Dust Samples from Kuwait and Iraq
Authors: Leski Tomasz A. , Malanoski Anthony P. , Gregory Michael J. , Lin Baochuan , Stenger David A.
Published: May 2011

A significant percentage of the human population is exposed to high levels of naturally occurring airborne dusts. Although the link between airborne particulate inhalation and a variety of respiratory diseases has long been established, little is known about the pathogenic role of the microbial component of the dust. In this study, we applied highly multiplexed PCR and a high-density resequencing microarray (RPM-TEI version 1.0) to screen samples of fine topsoil particles and airborne dust collected in 19 locations in Iraq and Kuwait for the presence of a broad range of human pathogens. The results indicated the presence of potential human pathogens, including
Mycobacterium
,
Brucella
,
Coxiella burnetii
,
Clostridium perfringens
, and
Bacillus
. The presence of
Coxiella burnetii
, a highly infectious potential biowarfare agent, was confirmed and detected in additional samples by use of a more sensitive technique (real-time PCR), indicating a high prevalence of this organism in the analyzed samples. The detection of potentially viable pathogens in breathable dusts from arid regions of Iraq and Kuwait underscores the importance of further study of these environments.
Genome Sequence of a Food Spoilage Lactic Acid Bacterium, Leuconostoc gasicomitatum LMG 18811
T
, in Association with Specific Spoilage Reactions
Authors: Johansson Per , Paulin Lars , Säde Elina , Salovuori Noora , Alatalo Edward R. , Björkroth K. Johanna , Auvinen Petri
Published: May 2011

Leuconostoc gasicomitatum
is a psychrotrophic lactic acid bacterium causing spoilage of cold-stored, modified-atmosphere-packaged (MAP), nutrient-rich foods. Its role has been verified by challenge tests in gas and slime formation, development of pungent acidic and buttery off odors, and greening of beef. MAP meats have especially been prone to
L. gasicomitatum
spoilage. In addition, spoilage of vacuum-packaged vegetable sausages and marinated herring has been reported. The genomic sequencing project of
L. gasicomitatum
LMG 18811
T
was prompted by a need to understand the growth and spoilage potentials of
L. gasicomitatum
, to study its phylogeny, and to be able to knock out and overexpress the genes. Comparative genomic analysis was done within
L. gasicomitatum
LMG 18811
T
and the three fully assembled
Leuconostoc
genomes (those of
Leuconostoc mesenteroides
,
Leuconostoc citreum
, and
Leuconostoc kimchii
) available. The genome of
L. gasicomitatum
LMG 18811
T
is plasmid-free and contains a 1,954,080-bp circular chromosome with an average GC content of 36.7%. It includes genes for the phosphoketolase pathway and alternative pathways for pyruvate utilization. As interesting features associated with the growth and spoilage potential, LMG 18811
T
possesses utilization strategies for ribose, external nucleotides, nucleosides, and nucleobases and it has a functional electron transport chain requiring only externally supplied heme for respiration. In respect of the documented specific spoilage reactions, the pathways/genes associated with a buttery off odor, meat greening, and slime formation were recognized. Unexpectedly, genes associated with platelet binding and collagen adhesion were detected, but their functionality and role in food spoilage and processing environment contamination need further study.
Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils
Authors: Yao Huaiying , Gao Yangmei , Nicol Graeme W. , Campbell Colin D. , Prosser James I. , Zhang Limei , Han Wenyan , Singh Brajesh K.
Published: May 2011

Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (
amoA
) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB
amoA
gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA
amoA
sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches.
New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina
Authors: Lamelas Araceli , Gosalbes María José , Moya Andrés , Latorre Amparo
Published: May 2011

The symbiotic association between aphids (Homoptera) and
Buchnera aphidicola
(
Gammaproteobacteria
) started about 100 to 200 million years ago. As a consequence of this relationship, the bacterial genome has undergone a prominent size reduction. The downsize genome process starts when the bacterium enters the host and will probably end with its extinction and replacement by another healthier bacterium or with the establishment of metabolic complementation between two or more bacteria. Nowadays, several complete genomes of
Buchnera aphidicola
from four different aphid species (
Acyrthosiphon pisum
,
Schizaphis graminum
,
Baizongia pistacea
, and
Cinara cedri
) have been fully sequenced.
C. cedri
belongs to the subfamily Lachninae and harbors two coprimary bacteria that fulfill the metabolic needs of the whole consortium:
B. aphidicola
with the smallest genome reported so far and “
Candidatus
Serratia symbiotica.” In addition,
Cinara tujafilina
, another member of the subfamily Lachninae, closely related to
C. cedri
, also harbors “
Ca.
Serratia symbiotica” but with a different phylogenetic status than the one from
C. cedri
. In this study, we present the complete genome sequence of
B. aphidicola
from
C. tujafilina
and the phylogenetic analysis and comparative genomics with the other
Buchnera
genomes. Furthermore, the gene repertoire of the last common ancestor has been inferred, and the evolutionary history of the metabolic losses that occurred in the different lineages has been analyzed. Although stochastic gene loss plays a role in the genome reduction process, it is also clear that metabolism, as a functional constraint, is also a powerful evolutionary force in insect endosymbionts.
Environmental Influences on Competitive Hydrogen Peroxide Production in Streptococcus gordonii
Authors: Zheng Lanyan , Itzek Andreas , Chen Zhiyun , Kreth Jens
Published: May 2011

Streptococcus gordonii
is an important member of the oral biofilm. One of its phenotypic traits is the production of hydrogen peroxide (H
2
O
2
). H
2
O
2
is an antimicrobial component produced by
S. gordonii
that is able to antagonize the growth of cariogenic
Streptococcus mutans
. Strategies that modulate H
2
O
2
production in the oral cavity may be useful as a simple therapeutic mechanism to improve oral health, but little is known about the regulation of H
2
O
2
production. The enzyme responsible for H
2
O
2
production is pyruvate oxidase, encoded by
spxB
. The functional studies of
spxB
expression and SpxB abundance presented in this report demonstrate a strong dependence on environmental oxygen tension and carbohydrate availability. Carbon catabolite repression (CCR) modulates
spxB
expression carbohydrate dependently. Catabolite control protein A (CcpA) represses
spxB
expression by direct binding to the
spxB
promoter, as shown by electrophoretic mobility shift assays (EMSA). Promoter mutation studies revealed the requirement of two catabolite-responsive elements (CRE) for CcpA-dependent
spxB
regulation, as evaluated by
spxB
expression and phenotypic H
2
O
2
production assays. Thus, molecular mechanisms for the control of
S. gordonii
spx
B
expression are presented for the first time, demonstrating the possibility of manipulating H
2
O
2
production for increased competitive fitness.
An Enzymatic Treatment of Soil-Bound Prions Effectively Inhibits Replication
Authors: Saunders Samuel E. , Bartz Jason C. , Vercauteren Kurt C. , Bartelt-Hunt Shannon L.
Published: May 2011

Chronic wasting disease (CWD) and scrapie can be transmitted through indirect environmental routes, possibly via soil, and a practical decontamination strategy for prion-contaminated soil is currently unavailable. In the laboratory, an enzymatic treatment under environmentally relevant conditions (22°C, pH 7.4) can degrade soil-bound PrP
Sc
below the limits of Western blot detection. We developed and used a quantitative serial protein misfolding cyclic amplification (PMCA) protocol to characterize the amplification efficiency of treated soil samples relative to controls of known infectious titer. Our results suggest large (10
4
- to >10
6
-fold) decreases in soil-bound prion infectivity following enzyme treatment, demonstrating that a mild enzymatic treatment could effectively reduce the risk of prion disease transmission via soil or other environmental surfaces.
Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)
Authors: Liu Fenyun , Kariyawasam Subhashinie , Jayarao Bhushan M. , Barrangou Rodolphe , Gerner-Smidt Peter , Ribot Efrain M. , Knabel Stephen J. , Dudley Edward G.
Published: May 2011

Salmonella enterica
subsp.
enterica
serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for
S
. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of
S
. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (
fimH
and
sseL
) and clustered regularly interspaced short palindromic repeats (CRISPRs)—CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)—was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of
S
. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on
fimH
and
sseL
identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of
S
. Enteritidis strains that contaminate chickens and eggs.
Population Dynamics of Salmonella enterica Serotypes in Commercial Egg and Poultry Production
Authors: Foley Steven L. , Nayak Rajesh , Hanning Irene B. , Johnson Timothy J. , Han Jing , Ricke Steven C.
Published: May 2011

Fresh and processed poultry have been frequently implicated in cases of human salmonellosis. Furthermore, increased consumption of meat and poultry has increased the potential for exposure to
Salmonella enterica
. While advances have been made in reducing the prevalence and frequency of
Salmonella
contamination in processed poultry, there is mounting pressure on commercial growers to prevent and/or eliminate these human pathogens in preharvest production facilities. Several factors contribute to
Salmonella
colonization in commercial poultry, including the serovar and the infectious dose. In the early 1900s,
Salmonella enterica
serovars Pullorum and Gallinarum caused widespread diseases in poultry, but vaccination and other voluntary programs helped eradicate pullorum disease and fowl typhoid from commercial flocks. However, the niche created by the eradication of these serovars was likely filled by
S.
Enteritidis, which proliferated in the bird populations. While this pathogen remains a significant problem in commercial egg and poultry production, its prevalence among poultry has been declining since the 1990s. Coinciding with the decrease of
S.
Enteritidis,
S.
Heidelberg and
S.
Kentucky have emerged as the predominant serovars in commercial broilers. In this review, we have highlighted bacterial genetic and host-related factors that may contribute to such shifts in
Salmonella
populations in commercial poultry and intervention strategies that could limit their colonization.
Disruption of the Termite Gut Microbiota and Its Prolonged Consequences for Fitness
Authors: Rosengaus Rebeca B. , Zecher Courtney N. , Schultheis Kelley F. , Brucker Robert M. , Bordenstein Seth R.
Published: May 2011

The disruption of host-symbiont interactions through the use of antibiotics can help elucidate microbial functions that go beyond short-term nutritional value. Termite gut symbionts have been studied extensively, but little is known about their impact on the termite's reproductive output. Here we describe the effect that the antibiotic rifampin has not only on the gut microbial diversity but also on the longevity, fecundity, and weight of two termite species,
Zootermopsis angusticollis
and
Reticulitermes flavipes
. We report three key findings: (i) the antibiotic rifampin, when fed to primary reproductives during the incipient stages of colony foundation, causes a permanent reduction in the diversity of gut bacteria and a transitory effect on the density of the protozoan community; (ii) rifampin treatment reduces oviposition rates of queens, translating into delayed colony growth and ultimately reduced colony fitness; and (iii) the initial dosages of rifampin had severe long-term fitness effects on
Z. angusticollis
. Taken together, our findings demonstrate that the antibiotic-induced perturbation of the microbial community is associated with prolonged reductions in longevity and fecundity. A causal relationship between these changes in the gut microbial population structures and fitness is suggested by the acquisition of opportunistic pathogens and incompetence of the termites to restore a pretreatment, native microbiota. Our results indicate that antibiotic treatment significantly alters the termite's microbiota, reproduction, colony establishment, and ultimately colony growth and development. We discuss the implications for antimicrobials as a new application to the control of termite pest species.
Role of “Dehalococcoides” spp. in the Anaerobic Transformation of Hexachlorobenzene in European Rivers
Authors: Taş Neslihan , van Eekert Miriam H. A. , Wagner Anke , Schraa Gosse , de Vos Willem M. , Smidt Hauke
Published: May 2011

The diffuse pollution by chlorinated organic compounds in river basins is a concern, due to their potential adverse effects on human health and the environment. Organohalides, like hexachlorobenzene (HCB), are recalcitrant to aerobic microbial degradation, and “Dehalococcoides” spp. are the only known microorganisms capable of anaerobic transformation of these compounds coupled to their growth. In this study, sediments from four European rivers were studied in order to determine their HCB dechlorination capacities and the role ofDehalococcoidesspp. in this process. Only a weak correlation was observed betweenDehalococcoidesspecies abundance and HCB transformation rates from different locations. In one of these locations, in the Ebro River sediment, HCB dechlorination could be linked toDehalococcoidesspecies growth and activity by 16S rRNA-based molecular methods. Furthermore, HCB dechlorination activity in this sediment was found over the full range of ambient temperatures that this sediment can be exposed to during different seasons throughout the year. The sediment contained several reductive dehalogenase (rdh) genes, and analysis of their transcription revealed the dominance ofcbrA, previously shown to encode a trichlorobenzene reductive dehalogenase. This study investigated the role ofDehalococcoidesspp. in HCB dechlorination in river sediments and evaluated if the current knowledge ofrdhgenes could be used to assess HCB bioremediation potential.
Enhancing the Stress Tolerance and Virulence of an Entomopathogen by Metabolic Engineering of Dihydroxynaphthalene Melanin Biosynthesis Genes
Authors: Tseng Min N. , Chung Pei C. , Tzean Shean S.
Published: May 2011

Entomopathogenic fungi have been used for biocontrol of insect pests for many decades. However, the efficacy of such fungi in field trials is often inconsistent, mainly due to environmental stresses, such as UV radiation, temperature extremes, and desiccation. To circumvent these hurdles, metabolic engineering of dihydroxynaphthalene (DHN) melanin biosynthetic genes (polyketide synthase, scytalone dehydratase, and 1,3,8-trihydroxynaphthalene reductase genes) cloned fromAlternaria alternatawere transformed into the amelanotic entomopathogenic fungusMetarhizium anisopliaeviaAgrobacterium-mediated transformation. Melanin expression in the transformant ofM. anisopliaewas verified by spectrophotometric methods, liquid chromatography/mass spectrometry (LC/MS), and confocal microscopy. The transformant, especially under stresses, showed notably enhanced antistress capacity and virulence, in terms of germination and survival rate, infectivity, and reduced median time to death (LT50) in killing diamondback moth (Plutella xylostella) larvae compared with the wild type. The possible mechanisms in enhancing the stress tolerance and virulence, and the significance and potential for engineering melanin biosynthesis genes in other biocontrol agents and crops to improve antistress fitness are discussed.
Involvement of the Azorhizobial Chromosome Partition Gene (
parA
) in the Onset of Bacteroid Differentiation during Sesbania rostrata Stem Nodule Development
Authors: Liu Chi-Te , Lee Kyung-Bum , Wang Yu-Sheng , Peng Min-Hua , Lee Kung-Ta , Suzuki Shino , Suzuki Tadahiro , Oyaizu Hiroshi
Published: May 2011

A
parA
gene in-frame deletion mutant of
Azorhizobium caulinodans
ORS571 (ORS571-ΔparA) was constructed to evaluate the roles of the chromosome-partitioning gene on various bacterial traits and on the development of stem-positioned nodules. The Δ
parA
mutant showed a pleiomorphic cell shape phenotype and was polyploid, with differences in nucleoid sizes due to dramatic defects in chromosome partitioning. Upon inoculation of the Δ
parA
mutant onto the stem of
Sesbania rostrata
, three types of immature nodule-like structures with impaired nitrogen-fixing activity were generated. Most showed signs of bacteroid early senescence. Moreover, the Δ
parA
cells within the nodule-like structures exhibited multiple developmental-stage phenotypes. Since the
bacA
gene has been considered an indicator for bacteroid formation, we applied the expression pattern of
bacA
as a nodule maturity index in this study. Our data indicate that the
bacA
gene expression is
parA
dependent in symbiosis. The presence of the
parA
gene transcript was inversely correlated with the maturity of nodule; the transcript was switched off in fully mature bacteroids. In summary, our experimental evidence demonstrates that the
parA
gene not only plays crucial roles in cellular development when the microbe is free-living but also negatively regulates bacteroid formation in
S. rostrata
stem nodules.
Environmental and Taxonomic Bacterial Diversity of Anaerobic Uranium(IV) Bio-Oxidation
Authors: Weber Karrie A. , Thrash J. Cameron , Van Trump J. Ian , Achenbach Laurie A. , Coates John D.
Published: May 2011

Microorganisms in diverse terrestrial surface and subsurface environments can anaerobically catalyze the oxidative dissolution of uraninite. While a limited quantity (∼5 to 12 μmol liter−1) of uranium is oxidatively dissolved in pure culture studies, the metabolism is coupled to electron transport, providing the potential of uraninite to support indigenous microbial populations and to solubilize uranium.
Unsuspected Diversity of Arsenite-Oxidizing Bacteria as Revealed by Widespread Distribution of theaoxBGene in Prokaryotes
Authors: Heinrich-Salmeron Audrey , Cordi Audrey , Brochier-Armanet Céline , Halter David , Pagnout Christophe , Abbaszadeh-fard Elham , Montaut Didier , Seby Fabienne , Bertin Philippe N. , Bauda Pascale , Arsène-Ploetze Florence
Published: May 2011

In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity ofaoxBgenes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterialaoxBgenes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading ofaoxBin prokaryotic communities.
Ubiquitylation and Developmental Regulation of Invariant Surface Protein Expression in Trypanosomes
Authors: Leung Ka Fai , Riley Fay S. , Carrington Mark , Field Mark C.
Published: May 2011

The cell surface of
Trypanosoma brucei
is dominated by the glycosylphosphatidylinositol-anchored variant surface glycoprotein (VSG), which is essential for immune evasion. VSG biosynthesis, trafficking, and turnover are well documented, but
trans
-membrane domain (TMD) proteins, including the invariant surface glycoproteins (ISGs), are less well characterized. Internalization and degradation of ISG65 depend on ubiquitylation of conserved cytoplasmic lysines. Using epitope-tagged ISG75 and reporter chimeric proteins bearing the cytoplasmic and
trans
-membrane regions of ISG75, together with multiple mutants with lysine-to-arginine mutations, we demonstrate that the cytoplasmic tail of ISG75 is both sufficient and necessary for endosomal targeting and degradation. The ISG75 chimeric reporter protein localized to endocytic organelles, while lysine-null versions were significantly stabilized at the cell surface. Importantly, ISG75 cytoplasmic lysines are modified by extensive oligoubiquitin chains and ubiquitylation is abolished in the lysine-null version. Furthermore, we find evidence for differential modes of turnover of ISG65 and ISG75. Full-length lysine-null ISG65 localization and protein turnover are significantly perturbed, but ISG75 localization and protein turnover are not, while ubiquitin conjugates can be detected for full-length lysine-null ISG75 but not ISG65. We find that the ISG75 ectodomain has a predicted coiled-coil, suggesting that ISG75 could be part of a complex, while ISG65 behaves independently. We also demonstrate a developmental stage-specific mechanism for exclusion of surface ISG expression in insect-stage cells by a ubiquitin-independent mechanism. We suggest that ubiquitylation may be a general mechanism for regulating
trans
-membrane domain surface proteins in trypanosomes.
TbISWI Regulates Multiple Polymerase I (Pol I)-Transcribed Loci and Is Present at Pol II Transcription Boundaries in Trypanosoma brucei
Authors: Stanne Tara M. , Kushwaha Manish , Wand Matthew , Taylor Jesse E. , Rudenko Gloria
Published: May 2011

The unicellular eukaryote
Trypanosoma brucei
is unusual in having very little transcriptional control. The bulk of the
T. brucei
genome is constitutively transcribed by RNA polymerase II (Pol II) as extensive polycistronic transcription units. Exceptions to this rule include several RNA Pol I transcription units such as the
VSG
expression sites (ESs), which are mono-allelically expressed. TbISWI, a member of the SWI2/SNF2 related chromatin remodeling ATPases, plays a role in repression of Pol I-transcribed ESs in both bloodstream- and procyclic-form
T. brucei
. We show that TbISWI binds both active and silent ESs but is depleted from the ES promoters themselves. TbISWI knockdown results in an increase in
VSG
transcripts from the silent
VSG
ESs. In addition to its role in the repression of the silent ESs, TbISWI also contributes to the downregulation of the Pol I-transcribed procyclin loci, as well as nontranscribed
VSG
basic copy arrays and minichromosomes. We also show that TbISWI is enriched at a number of strand switch regions which form the boundaries between Pol II transcription units. These strand switch regions are the presumed sites of Pol II transcription initiation and termination and are enriched in modified histones and histone variants. Our results indicate that TbISWI is a versatile chromatin remodeler that regulates transcription at multiple Pol I loci and is particularly abundant at many Pol II transcription boundaries in
T. brucei
.
The Essentiality of the Fungus-Specific Dam1 Complex Is Correlated with a One-Kinetochore-One-Microtubule Interaction Present throughout the Cell Cycle, Independent of the Nature of a Centromere
Authors: Thakur Jitendra , Sanyal Kaustuv
Published: May 2011

A fungus-specific outer kinetochore complex, the Dam1 complex, is essential in
Saccharomyces cerevisiae
, nonessential in fission yeast, and absent from metazoans. The reason for the reductive evolution of the functionality of this complex remains unknown. Both
Candida albicans
and
Schizosaccharomyces pombe
have regional centromeres as opposed to the short-point centromeres of
S. cerevisiae
. The interaction of one microtubule per kinetochore is established both in
S. cerevisiae
and
C. albicans
early during the cell cycle, which is in contrast to the multiple microtubules that bind to a kinetochore only during mitosis in
S. pombe
. Moreover, the Dam1 complex is associated with the kinetochore throughout the cell cycle in
S. cerevisiae
and
C. albicans
but only during mitosis in
S. pombe
. Here, we show that the Dam1 complex is essential for viability and indispensable for proper mitotic chromosome segregation in
C. albicans
. The kinetochore localization of the Dam1 complex is independent of the kinetochore-microtubule interaction, but the function of this complex is monitored by a spindle assembly checkpoint. Strikingly, the Dam1 complex is required to prevent precocious spindle elongation in premitotic phases. Thus, constitutive kinetochore localization associated with a one-microtubule-one kinetochore type of interaction, but not the length of a centromere, is correlated with the essentiality of the Dam1 complex.
New Cell Surface Protein Involved in Biofilm Formation by Streptococcus parasanguinis
Authors: Liang Xiaobo , Chen Yi-Ywan M. , Ruiz Teresa , Wu Hui
Published: May 2011

Dental biofilm formation is critical for maintaining the healthy microbial ecology of the oral cavity. Streptococci are predominant bacterial species in the oral cavity and play important roles in the initiation of plaque formation. In this study, we identified a new cell surface protein, BapA1, from
Streptococcus parasanguinis
FW213 and determined that BapA1 is critical for biofilm formation. Sequence analysis revealed that BapA1 possesses a typical cell wall-sorting signal for cell surface-anchored proteins from Gram-positive bacteria. No functional orthologue was reported in other streptococci. BapA1 possesses nine putative pilin isopeptide linker domains which are crucial for pilus assembly in a number of Gram-positive bacteria. Deletion of the 3′ portion of
bapA1
generated a mutant that lacks surface-anchored BapA1 and abolishes formation of short fibrils on the cell surface. The mutant failed to form biofilms and exhibited reduced adherence to an
in vitro
tooth model. The BapA1 deficiency also inhibited bacterial autoaggregation. The N-terminal muramidase-released-protein-like domain mediated BapA1-BapA1 interactions, suggesting that BapA1-mediated cell-cell interactions are important for bacterial autoaggregation and biofilm formation. Furthermore, the BapA1-mediated bacterial adhesion and biofilm formation are independent of a fimbria-associated serine-rich repeat adhesin, Fap1, demonstrating that BapA1 is a new streptococcal adhesin.
Scc1 (CP0432) and Scc4 (CP0033) Function as a Type III Secretion Chaperone for CopN of Chlamydia pneumoniae
Authors: Silva-Herzog Eugenia , Joseph Sabrina S. , Avery Ann K. , Coba Jose A. , Wolf Katerina , Fields Kenneth A. , Plano Gregory V.
Published: May 2011

The
Chlamydia pneumoniae
CopN protein is a member of the YopN/TyeA/InvE/MxiC family of secreted proteins that function to regulate the secretion of type III secretion system (T3SS) translocator and effector proteins. In this study, the Scc1 (CP0432) and Scc4 (CP0033) proteins of
C. pneumoniae
AR-39 were demonstrated to function together as a type III secretion chaperone that binds to an N-terminal region of CopN. The Scc1/Scc4 chaperone promoted the efficient secretion of CopN via a heterologous T3SS, whereas, the Scc3 chaperone, which binds to a C-terminal region of CopN, reduced CopN secretion.
Energy-Dependent Stability of Shewanella oneidensis MR-1 Biofilms
Authors: Saville Renee M. , Rakshe Shauna , Haagensen Janus A. J. , Shukla Soni , Spormann Alfred M.
Published: May 2011

Stability and resistance to dissolution are key features of microbial biofilms. How these macroscopic properties are determined by the physiological state of individual biofilm cells in their local physical-chemical and cellular environment is largely unknown. In order to obtain molecular and energetic insight into biofilm stability, we investigated whether maintenance of biofilm stability is an energy-dependent process and whether transcription and/or translation is required for biofilm dissolution. We found that in 12-hour-old
Shewanella oneidensis
MR-1 biofilms, a reduction in cellular ATP concentration, induced either by oxygen deprivation or by addition of the inhibitor of oxidative phosphorylation carbonyl cyanide
m
-chlorophenylhydrazone (CCCP), dinitrophenol (DNP), or CN
−
, resulted in massive dissolution. In 60-hour-old biofilms, the extent of uncoupler-induced cell loss was strongly attenuated, indicating that the integrity of older biofilms is maintained by means other than those operating in younger biofilms. In experiments with 12-hour-old biofilms, the transcriptional and translational inhibitors rifampin, tetracycline, and erythromycin were found to be ineffective in preventing energy starvation-induced detachment, suggesting that neither transcription nor translation is required for this process. Biofilms of
Vibrio cholerae
were also induced to dissolve upon CCCP addition to an extent similar to that in
S. oneidensis
. However,
Pseudomonas aeruginosa
and
P. putida
biofilms remained insensitive to CCCP addition. Collectively, our data show that metabolic energy is directly or indirectly required for maintaining cell attachment, and this may represent a common but not ubiquitous mechanism for stability of microbial biofilms.
The Key Sigma Factor of Transition Phase, SigH, Controls Sporulation, Metabolism, and Virulence Factor Expression in Clostridium difficile
Authors: Saujet Laure , Monot Marc , Dupuy Bruno , Soutourina Olga , Martin-Verstraete Isabelle
Published: May 2011

Toxin synthesis in
Clostridium difficile
increases as cells enter into stationary phase. We first compared the expression profiles of strain 630E during exponential growth and at the onset of stationary phase and showed that genes involved in sporulation, cellular division, and motility, as well as carbon and amino acid metabolism, were differentially expressed under these conditions. We inactivated the
sigH
gene, which encodes an alternative sigma factor involved in the transition to post-exponential phase in
Bacillus subtilis
. Then, we compared the expression profiles of strain 630E and the
sigH
mutant after 10 h of growth. About 60% of the genes that were differentially expressed between exponential and stationary phases, including genes involved in motility, sporulation, and metabolism, were regulated by SigH, which thus appears to be a key regulator of the transition phase in
C. difficile
. SigH positively controls several genes required for sporulation. Accordingly,
sigH
inactivation results in an asporogeneous phenotype. The
spo0A
and
CD2492
genes, encoding the master regulator of sporulation and one of its associated kinases, and the
spoIIA
operon were transcribed from a SigH-dependent promoter. The expression of
tcdA
and
tcdB
, encoding the toxins, and of
tcdR
, encoding the sigma factor required for toxin production, increased in a
sigH
mutant. Finally, SigH regulates the expression of genes encoding surface-associated proteins, such as the Cwp66 adhesin, the S-layer precursor, and the flagellum components. Among the 286 genes positively regulated by SigH, about 40 transcriptional units presenting a SigH consensus in their promoter regions are good candidates for direct SigH targets.
Complete Genome Sequence of Streptococcus suis Serotype 3 Strain ST3
Authors: Hu Pan , Yang Ming , Zhang Anding , Wu Jiayan , Chen Bo , Hua Yafeng , Yu Jun , Chen Huanchun , Xiao Jingfa , Jin Meilin
Published: May 2011

Streptococcus suis
is a zoonotic pathogen causing economic loss in the swine industry and is also a threat to human health. To date, the mechanism of pathogenesis is not fully understood. Here, we report the complete genome sequence of
S. suis
strain ST3 of serotype 3, which provides opportunities to reveal genetic basis of infection of
S. suis
non-serotype 2 strains.
Genome Sequence of Strain IMCC9480, a Xanthorhodopsin-Bearing Betaproteobacterium Isolated from the Arctic Ocean
Authors: Oh Hyun-Myung , Lee Kiyoung , Jang Yoonra , Kang Ilnam , Kim Hee-Jin , Kang Tae-Wook , Kim Seon-Young , Cho Jang-Cheon
Published: May 2011

Strain IMCC9480 is a novel member of the family
Oxalobacteraceae
of the
Betaproteobacteria
, isolated from the Arctic Ocean by dilution-to-extinction culturing. Here we present the draft genome sequence of strain IMCC9480. The genome is predicted to contain genes for xanthorhodopsin, retinoid biosynthesis, carbon monoxide dehydrogenase, and C
1
metabolism.
The role of relationships in improving early diagnosis of prostate cancer
Authors: Forbat L , Hubbard G , Place M , Boyd K , Leung H , Winslow F , Kelly D
Published: May 2011

Introduction

Early diagnosis is critical in reducing mortality in prostate cancer. The extant literature identifies a range of variables which impact on when men present in primary care. For example, recent evidence suggests that men from high deprivation areas are significantly more likely to present with advanced disease and have lower survival rates. Psychosocial theories provide a framework for understanding patterns in the timing of diagnoses, for example, the role of social context and relationships in help-seeking behaviour.

Aim

To identify how men account for the timing of their presentation and subsequent diagnosis with advanced disease.

Methods

Embedded mixed-method design involving a postal survey (N=320) and semi-structured interviews with a purposive sub-sample of men and partners (N=30). Analysis drew primarily on χ2and spearman's correlation, alongside framework analysis of the qualitative data, informed by Anderson's (1995) model of Total Patient Delay.

Results

Data indicate that relationships and experiential knowledge play significant roles in gaining a diagnosis. Notably friends/relatives are key sources of information on prostate cancer and often prompt help-seeking behaviour. Indeed, men's perceptions of risk are not informed by clinical risk factors such as age and family history, but by their own and friends/relatives' experiential knowledge.

Conclusion

Health promotion interventions should draw on relational theories, to be cognisant of the important role of relationships in help-seeking behaviour. Adopting a systemic approach has the potential to reach men at higher risk of prostate cancer and contribute to earlier diagnosis.
Evaluation and implementation of an intervention to promote early presentation
Authors: Forster A S , Forbes L J L , Atkins L , Patnick J , Sellars S , Tucker L , Baxter R , Ramirez A J
Published: May 2011

Introduction and aims

Older women are more likely to delay presentation in breast cancer,1 which in turn contributes to poorer survival.2 We have developed a health professional-delivered intervention to promote early presentation in older women with breast symptoms (Promoting Early Presentation (PEP) Intervention) to be delivered when they attend for their final routine mammogram. We aimed to evaluate its efficacy in an randomized controlled trial (RCT) and adapt it for use in routine clinical practice.

Methods

We randomised 867 women attending for their final round of screening on the NHS Breast Screening Programme to receive either the PEP Intervention delivered by a radiographer or usual care. We measured breast cancer awareness at baseline and 2 years post-randomisation. We are adapting and piloting the PEP Intervention to be suitable for adoption in routine practice across the NHS Breast Screening Programme.

Results

In the RCT, the PEP Intervention increased the proportion breast cancer aware at 2 years compared with usual care (21% vs 6%, OR: 8.1, 95% CI: 2.7 to 25.0). We have adapted the intervention so that it can be delivered feasibly while maintaining consistent quality.

Conclusions

We have demonstrated the efficacy of the PEP Intervention in an RCT. We plan to evaluate its effectiveness in routine practice by implementing it in three breast screening services, and measuring feasibility, costs and health outcomes (comparing these with health outcomes in control services). Our findings will provide the data needed to inform possible implementation across the entire NHS Breast Screening Programme.
The use of a modified ‘surprise’ question to identify and recruit dying patients into a research project
Authors: Forbes K , Gibbins J , Burcombe M E , Bloor S J , Reid C M , McCoubrie R C , Kinzel C , King S
Published: May 2011

Introduction and aims

To improve end-of-life care we need good evidence. The challenges of carrying out research with patients who are dying are well documented yet this research is vital to determine whether new interventions improve care. We examined the feasibility of recruiting patients into a study examining their care as they died.

Methods

We performed a prospective mixed-methods observational study of the care given to patients who were dying. All patients on study wards were screened on admission using the question ‘Is this patient so unwell you feel they could die on this admission?’ If the answer was ‘yes’ the patient (and/or family) was approached to give prior consent to being included in the study ‘should they become more unwell’.

Results

Over 2 years, 6703 patients were screened; staff answered ‘yes’ to the screening question for 327 patients (5%). Prior consent (23) or relative assent (94) was obtained for 117 (36%) of these patients. 70 died within the study. Overall, the screening question had a sensitivity of 57% and a specificity of 98%.

Conclusion

To our knowledge prior consent for research during the dying process has not been used before within an acute trust. While a large number of patients need to be screened, we have shown that a modified surprise question is helpful in identifying patients who will die during an admission, and it is feasible to gain consent from these patients, or assent from their relatives, for inclusion in a study to examine the dying process.
Education in advanced disease: professionals' knowledge, attitudes and ability
Authors: Flemming K , Closs S J , Foy R , Bennett M I
Published: May 2011

Introduction and aims

The management of symptoms and lifestyle in advanced disease are essential for the maintenance of patients' quality of life. Health care professionals can facilitate patients to optimise disease management by providing appropriate education. While the provision of education by health professionals for patients with advanced cancer is reasonably well documented, less attention has been paid to other advancing progressive diseases. The aim of this review was to synthesise qualitative research which examined health care professionals' knowledge, attitudes and ability towards delivering educational interventions to patients with the following advanced progressive diseases: heart failure, chronic respiratory disease, end stage renal disease and neuromuscular disorders.

Methods

The synthesis was conducted using meta-ethnography. Systematic searching of five electronic databases (CINAHL, Medline, PsychInfo, Web of Science Social Science Citation Index and EMBASE) occurred. Included papers were data extracted and assessed for quality.

Results

The searches identified 911 records, of which 17 met the inclusion criteria for the review. Three key themes influencing the delivery of education to patients with advanced disease were identified:

Capacity (to educate and aid decision-making)

Context (of educational delivery)

Timing (of education).

Conclusion

A range of enablers and barriers identified by health care professionals influence their ability to deliver education at the end of life. Therefore, any interventions to change practice need to have multiple components, rather than targeting sole aspects such as knowledge or motivation alone. Strategies for improving educational practice should explicitly target factors judged as important and potentially amenable to change.