bluuebunny/crossref_metadata_2025 huggingface dataset:
GROWTH, EMPLOYMENT AND DISTRIBUTION IMPACTS OF MINERALS DEPENDENCY: FOUR CASE STUDIES
Authors: Berry Albert
Published: October 2008

Cross‐country evidence on the direct and indirect impacts of minerals dependency on growth suggests that the typical effect may be negative, and the experience in some countries implies large negative effects. The impact on employment and income distribution is even more likely to be adverse, since many minerals generate few jobs directly and may destroy more indirectly. Thus, countries heavily endowed with exportable natural resources cannot take it for granted that this condition will put them on a sustained and equitable development path. This study focuses on four countries – Indonesia, Chile, Venezuela and Nigeria – and looks at how they have handled export bonanzas, with focus on the employment as well as the growth fall‐out. The big policy questions are: what is the best way for a country to use its mineral resources to achieve equitable development, and is there a significant role for industrial strategy in identifying new comparative advantages or can markets do a better job relatively unimpeded? The four case studies reviewed here suggest that, depending on the specifics of the country, promising new comparative advantages can emerge in the primary, secondary and tertiary sectors, while the role of service tradables should not be discounted. It is intriguing that the great majority of minerals‐dependent countries to achieve sustained growth have also made significant progress in manufacturing. In a world that now penalises trade protectionism, the exchange rate can be a powerful tool to provide more neutral incentives for new tradables; indeed, one of the most striking features of the two success stories related here has been these countries' timely use of currency devaluations to achieve highly competitive exchange rates. The experiences of the four countries further confirm the risks of focusing on capital‐intensive industries in labour‐surplus countries, as well as the risk of lodging such activities in the public sector. Only Indonesia of the four countries was able to achieve good enough employment growth under mineral dependency to avoid a high or rising level of inequality. Clearly the challenge on the employment/distribution front is severe.
Spinal cord injury‐induced attenuation of GABAergic inhibition in spinal dorsal horn circuits is associated with down‐regulation of the chloride transporter KCC2 in rat
Authors: Lu Yan , Zheng Jihong , Xiong Lize , Zimmermann Manfred , Yang Jing
Published: October 2008

Most spinal cord injury (SCI) patients suffer from chronic pain. Effective therapy for this pain is lacking, and the underlying mechanisms are poorly understood. The spinal superficial dorsal horn (SDH) contains neuronal circuits capable of modulating primary afferent information involved in pain processing. KCC2 is an isoform of the K+–Cl− cotransporter that contributes to the regulation of transmembrane anion gradient which plays a key role in shaping GABAA receptor‐mediated signalling in the CNS. We tested the hypothesis that SCI causes down‐regulation of KCC2 distal to the injury and contributes to the neuronal hyperresponsiveness and pain‐related behaviours. SCI was a hemisection at T13 level of adult Sprague–Dawley rats. Spinal sagittal slices with attached dorsal roots (DR) were prepared from L4 to L6 level. The reversal potentials of GABA responses (EGABA) and DR‐evoked IPSPs and EPSPs of L4‐6 SDH neurones in sham‐operated and SCI rats were compared using gramicidin‐perforated patch‐clamp recordings. Here we report that thoracic SCI‐induced down‐regulation of KCC2 in the lumbar SDH parallels the development of allodynia. The subsequent changes of EGABA in SDH neurones attenuate the GABAA receptor‐mediated inhibitory synaptic transmission. These changes cause certain normally subthreshold primary A and C fibre inputs to evoke action potential output in SDH neurones. We conclude that SCI induces KCC2 down‐regulation and subsequent changes of EGABA in the SDH below the injury site. The resulting disinhibition unmasks normally ineffective SDH neuronal circuits and may contribute to the below‐level central pain‐related behaviours after incomplete SCI.
Noradrenaline triggers muscle tone by amplifying glutamate‐driven excitation of somatic motoneurones in anaesthetized rats
Authors: Schwarz Peter B. , Yee Nicole , Mir Saba , Peever John H.
Published: October 2008

Postural muscle tone is potently suppressed during sleep and cataplexy. Since brainstem noradrenergic cell discharge activity is tightly coupled with state‐dependent changes in muscle activity, it is assumed that noradrenergic drive on to somatic motoneurones modulates basal muscle tone. However, it has never been determined whether noradrenergic neurotransmission acts to directly regulate motoneurone activity or whether it functions to modulate prevailing synaptic activity. This is an important distinction because noradrenaline regulates cell excitability by both directly depolarizing neurones and by indirectly potentiating glutamate‐mediated excitation. We used reverse‐microdialysis, electrophysiology, neuro‐pharmacological and histological techniques in anaesthetized rats to determine whether strengthening noradrenergic drive (via exogenous noradrenaline application) on to trigeminal motoneurones affects masseter muscle tone by increasing spontaneous motoneurone activity or whether it acts to amplify prevailing glutamate‐driven excitation. Although noradrenaline is hypothesized to modulate motor activity, we found that direct stimulation of trigeminal motoneurones by α1‐adrenoceptor activation had no direct effect on basal masseter tone. However, when glutamate‐driven excitation was increased at the trigeminal motor pool by either endogenous glutamate release (induced by the monosynaptic masseteric reflex) or exogenous AMPA application, noradrenaline triggered a potent increase in basal masseter tone. The stimulatory effects of noradrenaline were unmasked and rapidly switched on only in the presence of glutamatergic transmission. Blockade of AMPA receptors abolished this excitatory effect, indicating that noradrenergic drive requires ongoing glutamatergic activity. Our data indicate that exogenous noradrenergic drive does not directly affect spontaneous motoneurone discharge activity in anaesthetized rats; rather, it triggers postural muscle tone by amplifying prevailing glutamate‐driven excitation.
AMPK‐independent pathways regulate skeletal muscle fatty acid oxidation
Authors: Dzamko Nicolas , Schertzer Jonathan D. , Ryall James G. , Steel Rohan , Macaulay S. Lance , Wee Sheena , Chen Zhi‐Ping , Michell Belinda J. , Oakhill Jonathan S. , Watt Matthew J. , Jørgensen Sebastian Beck , Lynch Gordon S. , Kemp Bruce E. , Steinberg Gregory R.
Published: October 2008

The activation of AMP‐activated protein kinase (AMPK) and phosphorylation/inhibition of acetyl‐CoA carboxylase 2 (ACC2) is believed to be the principal pathway regulating fatty acid oxidation. However, during exercise AMPK activity and ACC Ser‐221 phosphorylation does not always correlate with rates of fatty acid oxidation. To address this issue we have investigated the requirement for skeletal muscle AMPK in controlling aminoimidazole‐4‐carboxymide‐1‐β‐d‐ribofuranoside (AICAR) and contraction‐stimulated fatty acid oxidation utilizing transgenic mice expressing a muscle‐specific kinase dead (KD) AMPK α2. In wild‐type (WT) mice, AICAR and contraction increased AMPK α2 and α1 activities, the phosphorylation of ACC2 and rates of fatty acid oxidation while tending to reduce malonyl‐CoA levels. Despite no activation of AMPK in KD mice, ACC2 phosphorylation was maintained, malonyl‐CoA levels were reduced and rates of fatty acid oxidation were comparable between genotypes. During treadmill exercise both KD and WT mice had similar values of respiratory exchange ratio. These studies suggested the presence of an alternative ACC2 kinase(s). Using a phosphoproteomics‐based approach we identified 18 Ser/Thr protein kinases whose phosphorylation was increased by greater than 25% in contracted KD relative to WT muscle. Utilizing bioinformatics we predicted that extracellular regulated protein‐serine kinase (ERK1/2), inhibitor of nuclear factor (NF)‐κB protein‐serine kinase β (IKKβ) and protein kinase D (PKD) may phosphorylate ACC2 at Ser‐221 but during in vitro phosphorylation assays only AMPK phosphorylated ACC2. These data demonstrate that AMPK is not essential for the regulation of fatty acid oxidation by AICAR or muscle contraction.
Hypoxic preconditioning protects rat hearts against ischaemia–reperfusion injury: role of erythropoietin on progenitor cell mobilization
Authors: Lin Jih‐Shyong , Chen Yih‐Sharng , Chiang Han‐Sun , Ma Ming‐Chieh
Published: October 2008

Preconditioning, such as by brief hypoxic exposure, has been shown to protect hearts against severe ischaemia. Here we hypothesized that hypoxic preconditioning (HPC) protects injured hearts by mobilizing the circulating progenitor cells. Ischaemia–reperfusion (IR) injury was induced by left coronary ligation and release in rats kept in room air or preconditioned with 10% oxygen for 6 weeks. To study the role of erythropoietin (EPO), another HPC + IR group was given an EPO receptor (EPOR) antibody via a subcutaneous mini‐osmotic pump 3 weeks before IR induction. HPC alone gradually increased haematocrit, cardiac and plasma EPO, and cardiac vascular endothelial growth factor (VEGF) only in the first two weeks. HPC improved heart contractility, reduced ischaemic injury, and maintained EPO and EPOR levels in the infarct tissues of IR hearts, but had no significant effect on VEGF. Interestingly, the number of CD34+CXCR4+ cells in the peripheral blood and their expression in HPC‐treated hearts was higher than in control. Preconditioning up‐regulated cardiac expression of stromal derived factor‐1 (SDF‐1) and prevented its IR‐induced reduction. The EPOR antibody abolished HPC‐mediated functional recovery, and reduced SDF‐1, CXCR4 and CD34 expression in IR hearts, as well as the number of CD34+CXCR4+ cells in blood. The specificity of neutralizing antibody was confirmed in an H9c2 culture system. In conclusion, exposure of rats to moderate hypoxia leads to an increase in progenitor cells in the heart and circulation. This effect is dependent on EPO, which induces cell homing by increased SDF‐1/CXCR4 and reduces the heart susceptibly to IR injury.
Control of the single channel conductance of K2P10.1 (TREK‐2) by the amino‐terminus: role of alternative translation initiation
Authors: Simkin Dina , Cavanaugh Eric J. , Kim Donghee
Published: October 2008

TREK‐2 expressed in mammalian cells exhibits small (∼52 pS) and large (∼220 pS) unitary conductance levels. Here we tested the role of the N‐terminus (69 amino acids long) in the control of the unitary conductance, and role of the alternative translation initiation as a mechanism that produces isoforms of TREK‐2 that show different conductance levels. Deletion of the first half (Δ1–36) of the N‐terminus had no effect. However, deletion of most of the N‐terminus (Δ1–66) resulted in the appearance of only the large‐conductance channel (∼220 pS). In support of the critical function of the distal half of the N‐terminus, the deletion mutants Δ1–44 and Δ1–54 produced ∼90 pS and 188 pS channels, respectively. In Western blot analysis, TREK‐2 antibody detected two immunoreactive bands at ∼54 kDa and ∼60 kDa from cells expressing wild‐type TREK‐2 that has three potential translation initiation sites (designated M1M2M3) within the N‐terminus. Mutation of the second and third initiation sites from Met to Leu (M1L2L3) produced only the ∼60 kDa isoform and the small‐conductance channel (∼52 pS). Mutants designed to produce translation from the second (M2L3) or third (M3) initiation site produced the ∼54 kDa isoform, and the large conductance channel (∼185–224 pS). M1L2L3, M2L3 and M3 were relatively selectively permeable to K+, as judged by the 51–55 mV shifts in reversal potential following a 10‐fold change in [K+]o. PNa/PK values were also similar for M1L2L3 (∼0.02), M2L3 (∼0.02) and M3 (∼0.03). Arachidonic acid, proton and membrane stretch activated, whereas dibutyryl‐cAMP inhibited all three isoforms of TREK‐2, indicating that deletion of the N‐terminus does not abolish modulation. These results show that the small and large conductance TREK‐2 channels are produced as a result of alternative translation initiation, producing isoforms with long and short N‐termini, and that the distal half of the N‐terminus controls the unitary conductance.
Multi-University Research Teams: Shifting Impact, Geography, and Stratification in Science
Authors: Jones Benjamin F. , Wuchty Stefan , Uzzi Brian
Published: October 2008

This paper demonstrates that teamwork in science increasingly spans university boundaries, a dramatic shift in knowledge production that generalizes across virtually all fields of science, engineering, and social science. Moreover, elite universities play a dominant role in this shift. By examining 4.2 million papers published over three decades, we found that multi-university collaborations (i) are the fastest growing type of authorship structure, (ii) produce the highest-impact papers when they include a top-tier university, and (iii) are increasingly stratified by in-group university rank. Despite the rising frequency of research that crosses university boundaries, the intensification of social stratification in multi-university collaborations suggests a concentration of the production of scientific knowledge in fewer rather than more centers of high-impact science.
CTLA-4 Control over Foxp3
+
Regulatory T Cell Function
Authors: Wing Kajsa , Onishi Yasushi , Prieto-Martin Paz , Yamaguchi Tomoyuki , Miyara Makoto , Fehervari Zoltan , Nomura Takashi , Sakaguchi Shimon
Published: October 2008

Naturally occurring Foxp3
+
CD4
+
regulatory T cells (Tregs) are essential for maintaining immunological self-tolerance and immune homeostasis. Here, we show that a specific deficiency of cytotoxic T lymphocyte antigen 4 (CTLA-4) in Tregs results in spontaneous development of systemic lymphoproliferation, fatal T cell–mediated autoimmune disease, and hyperproduction of immunoglobulin E in mice, and it also produces potent tumor immunity. Treg-specific CTLA-4 deficiency impairs in vivo and in vitro suppressive function of Tregs—in particular, Treg-mediated down-regulation of CD80 and CD86 expression on dendritic cells. Thus, natural Tregs may critically require CTLA-4 to suppress immune responses by affecting the potency of antigen-presenting cells to activate other T cells.
Implications of Magma Transfer Between Multiple Reservoirs on Eruption Cycling
Authors: Elsworth Derek , Mattioli Glen , Taron Joshua , Voight Barry , Herd Richard
Published: October 2008

Volcanic eruptions are episodic despite being supplied by melt at a nearly constant rate. We used histories of magma efflux and surface deformation to geodetically image magma transfer within the deep crustal plumbing of the Soufrière Hills volcano on Montserrat, West Indies. For three cycles of effusion followed by discrete pauses, supply of the system from the deep crust and mantle was continuous. During periods of reinitiated high surface efflux, magma rose quickly and synchronously from a deflating mid-crustal reservoir (at about 12 kilometers) augmented from depth. During repose, the lower reservoir refilled from the deep supply, with only minor discharge transiting the upper chamber to surface. These observations are consistent with a model involving the continuous supply of magma from the deep crust and mantle into a voluminous and compliant mid-crustal reservoir, episodically valved below a shallow reservoir (at about 6 kilometers).
Small Molecule-Induced Allosteric Activation of the
Vibrio cholerae
RTX Cysteine Protease Domain
Authors: Lupardus Patrick J. , Shen Aimee , Bogyo Matthew , Garcia K. Christopher
Published: October 2008

Vibrio cholerae
RTX (repeats in toxin) is an actin-disrupting toxin that is autoprocessed by an internal cysteine protease domain (CPD). The RTX CPD is efficiently activated by the eukaryote-specific small molecule inositol hexakisphosphate (InsP
6
), and we present the 2.1 angstrom structure of the RTX CPD in complex with InsP
6
. InsP
6
binds to a conserved basic cleft that is distant from the protease active site. Biochemical and kinetic analyses of CPD mutants indicate that InsP
6
binding induces an allosteric switch that leads to the autoprocessing and intracellular release of toxin-effector domains.
Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA
Authors: Moritz Craig , Patton James L. , Conroy Chris J. , Parra Juan L. , White Gary C. , Beissinger Steven R.
Published: October 2008

We provide a century-scale view of small-mammal responses to global warming, without confounding effects of land-use change, by repeating Grinnell's early–20th century survey across a 3000-meter-elevation gradient that spans Yosemite National Park, California, USA. Using occupancy modeling to control for variation in detectability, we show substantial (∼500 meters on average) upward changes in elevational limits for half of 28 species monitored, consistent with the observed ∼3°C increase in minimum temperatures. Formerly low-elevation species expanded their ranges and high-elevation species contracted theirs, leading to changed community composition at mid- and high elevations. Elevational replacement among congeners changed because species' responses were idiosyncratic. Though some high-elevation species are threatened, protection of elevation gradients allows other species to respond via migration.
Generation of Mouse Induced Pluripotent Stem Cells Without Viral Vectors
Authors: Okita Keisuke , Nakagawa Masato , Hyenjong Hong , Ichisaka Tomoko , Yamanaka Shinya
Published: October 2008

Induced pluripotent stem (iPS) cells have been generated from mouse and human somatic cells by introducing Oct3/4 and Sox2 with either Klf4 and c-Myc or Nanog and Lin28 using retroviruses or lentiviruses. Patient-specific iPS cells could be useful in drug discovery and regenerative medicine. However, viral integration into the host genome increases the risk of tumorigenicity. Here, we report the generation of mouse iPS cells without viral vectors. Repeated transfection of two expression plasmids, one containing the complementary DNAs (cDNAs) of Oct3/4, Sox2, and Klf4 and the other containing the c-Myc cDNA, into mouse embryonic fibroblasts resulted in iPS cells without evidence of plasmid integration, which produced teratomas when transplanted into mice and contributed to adult chimeras. The production of virus-free iPS cells, albeit from embryonic fibroblasts, addresses a critical safety concern for potential use of iPS cells in regenerative medicine.
Arguing for Embodied Consciousness
Authors: Fromm Harold
Published: October 2008

What Science Offers the Humanities
. Integrating Body and Culture.
By Edward Slingerland
. Cambridge University Press, New York, 2008. 388 pp. $85, £45. ISBN 9780521877701. Paper, $24.99, £18.99. ISBN 9780521701518.

The author argues that findings from the natural sciences, especially research on human cognition, are critical to progress in the humanities and studies of culture.
Subject Matter Matters
Authors: Parrish Mary
Published: October 2008

Humans, Nature, and Birds
. Science Art from Cave Walls to Computer Screens.
By Darryl Wheye and Donald Kennedy
. Yale University Press, New Haven, CT, 2008. 229 pp. $37.50, £25. ISBN 9780300123883.

A History of Paleontology Illustration
.
By Jane P. Davidson
. Indiana University Press, Bloomington, 2008. 235 pp. $39.95. ISBN 9780253351753.

These two books will fascinate readers interested in the arena in which art and science come together or in illustrations of birds or fossils.
Calling All Dancing Scientists!
Authors: Bohannon John
Published: October 2008

If you missed this year's "Dance Your Ph.D." contest, act fast: The deadline to enter the 2009 contest, for which the stage will be much larger and the prize far grander, is 16 November 2008.
Phylogenetic Relationships and Functional Genes: Distribution of a Gene (
mnxG
) Encoding a Putative Manganese-Oxidizing Enzyme in
Bacillus
Species
Authors: Mayhew Lisa E. , Swanner Elizabeth D. , Martin Andy P. , Templeton Alexis S.
Published: October 2008

Several
Bacillus
and
Paenibacillus
species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the
mnxG
gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in
Bacillus
species. Seven of eight
Bacillus
species were capable of Mn(II) oxidation; however, the
mnxG
gene was detected in only one isolate. Using sequences of known
Bacillus
species both with and without amplifiable
mnxG
genes and Henderson Mine isolates, the 16S rRNA and
mnxG
gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable
mnxG
gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable
mnxG
gene in the isolates. The data revealed a complex phylogenetic distribution of the
mnxG
gene in which vertical inheritance and gene loss influence the distribution of the gene among the
Bacillus
species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the
mnxG
gene within the
Bacillus
clade.
Identification of
Bacillus cereus
Group Species Associated with Food Poisoning Outbreaks in British Columbia, Canada
Authors: McIntyre Lorraine , Bernard Kathryn , Beniac Daniel , Isaac-Renton Judith L. , Naseby David Craig
Published: October 2008

Food poisoning laboratories identify
Bacillus cereus
using routine methods that may not differentiate all
Bacillus cereus
group species. We recharacterized
Bacillus
food-poisoning strains from 39 outbreaks and identified
B. cereus
in 23 outbreaks,
B. thuringiensis
in 4,
B. mycoides
in 1, and mixed strains of
Bacillus
in 11 outbreaks.
Use of Flow Cytometry To Monitor
Legionella
Viability
Authors: Allegra Séverine , Berger Françoise , Berthelot Philippe , Grattard Florence , Pozzetto Bruno , Riffard Serge
Published: October 2008

Legionella
viability was monitored during heat shock treatment at 70°C by a flow cytometric assay (FCA). After 30 min of treatment, for 6 of the 12 strains tested, the FCA still detected 10 to 25% of cells that were viable but nonculturable (VBNC). These VBNC cells were able to produce ATP and to be resuscitated after culture on amoebae.
Transcriptional Analysis of
Clostridium beijerinckii
NCIMB 8052 and the Hyper-Butanol-Producing Mutant BA101 during the Shift from Acidogenesis to Solventogenesis
Authors: Shi Zhen , Blaschek Hans P.
Published: October 2008

Clostridium beijerinckii
is an anaerobic bacterium used for the fermentative production of acetone and butanol. The recent availability of genomic sequence information for
C. beijerinckii
NCIMB 8052 has allowed for an examination of gene expression during the shift from acidogenesis to solventogenesis over the time course of a batch fermentation using a ca. 500-gene set DNA microarray. The microarray was constructed using a collection of genes which are orthologs of members of gene families previously found to be important to the physiology of
C. acetobutylicum
ATCC 824. Similar to the onset of solventogenesis in
C. acetobutylicum
824, the onset of solventogenesis in
C. beijerinckii
8052 was concurrent with the initiation of sporulation. However, forespores and endospores developed more rapidly in
C. beijerinckii
8052 than in
C. acetobutylicum
824, consistent with the accelerated expression of the
sigE
- and
sigG
-regulated genes in
C. beijerinckii
8052. The comparison of gene expression patterns and morphological changes in
C. beijerinckii
8052 and the hyper-butanol-producing
C. beijerinckii
strain BA101 indicated that BA101 was less efficient in sporulation and phosphotransferase system-mediated sugar transport than 8052 but that it exhibited elevated expression of several primary metabolic genes and chemotaxis/motility genes.
Differential Expression in
Phanerochaete chrysosporium
of Membrane-Associated Proteins Relevant to Lignin Degradation
Authors: Shary Semarjit , Kapich Alexander N. , Panisko Ellen A. , Magnuson Jon K. , Cullen Daniel , Hammel Kenneth E.
Published: October 2008

Fungal lignin-degrading systems likely include membrane-associated proteins that participate in diverse processes such as uptake and oxidation of lignin fragments, production of ligninolytic secondary metabolites, and defense of the mycelium against ligninolytic oxidants. Little is known about the nature or regulation of these membrane-associated components. We grew the white rot basidiomycete
Phanerochaete chrysosporium
on cellulose or glucose as the carbon source and monitored the mineralization of a
14
C-labeled synthetic lignin by these cultures to assess their ligninolytic competence. The results showed that the cellulose-grown cultures were ligninolytic, whereas the glucose-grown ones were not. We isolated microsomal membrane fractions from both types of culture and analyzed tryptic digests of their proteins by shotgun liquid chromatography-tandem mass spectrometry. Comparison of the results against the predicted
P. chrysosporium
proteome showed that a catalase (Joint Genome Institute
P. chrysosporium
protein identification number [I.D.] 124398), an alcohol oxidase (126879), two transporters (137220 and 132234), and two cytochrome P450s (5011 and 8912) were upregulated under ligninolytic conditions. Quantitative reverse transcription-PCR assays showed that RNA transcripts encoding all of these proteins were also more abundant in ligninolytic cultures. Catalase 124398, alcohol oxidase 126879, and transporter 137220 were found in a proteomic analysis of partially purified plasma membranes from ligninolytic
P. chrysosporium
and are therefore most likely associated with the outer envelope of the fungus.
Case Series Study of Traveler's Diarrhea in U.S. Military Personnel at Incirlik Air Base, Turkey
Authors: Porter C. K. , El Mohammady H. , Baqar S. , Rockabrand D. M. , Putnam S. D. , Tribble D. R. , Riddle M. S. , Frenck R. W. , Rozmajzl P. , Kilbane E. , Fox A. , Ruck R. , Lim M. , Johnston Y. J. , Murphy E. , Sanders J. W.
Published: October 2008

Military personnel with traveler's diarrhea (
n
= 202) while deployed to Incirlik Air Base, Turkey, from June to September 2002 were evaluated for pathogen-specific immune responses. Serologic and fecal immunoglobulin A (IgA) titers to enterotoxigenic
Escherichia coli
antigens (CS6, CS3, and LT) were quite low. In contrast, subjects with
Campylobacter
infections had high serologic and fecal IgA responses.
Characterization of the Genomes of a Diverse Collection of
Salmonella enterica
Serovar Typhimurium Definitive Phage Type 104
Authors: Cooke Fiona J. , Brown Derek J. , Fookes Maria , Pickard Derek , Ivens Alasdair , Wain John , Roberts Mark , Kingsley Robert A. , Thomson Nicholas R. , Dougan Gordon
Published: October 2008

Salmonella enterica
serovar Typhimurium definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We completed the full DNA sequence of one DT104 strain, NCTC13348, and showed that significant differences between the genome of this isolate and the genome of the previously sequenced strain
Salmonella
serovar Typhimurium LT2 are due to integrated prophage elements and
Salmonella
genomic island 1 encoding antibiotic resistance genes. Thirteen isolates of
Salmonella
serovar Typhimurium DT104 with different pulsed-field gel electrophoresis (PFGE) profiles were analyzed by using multilocus sequence typing (MLST), plasmid profiling, hybridization to a pan-
Salmonella
DNA microarray, and prophage-based multiplex PCR. All the isolates belonged to a single MLST type, sequence type ST19. Microarray data demonstrated that the gene contents of the 13 DT104 isolates were remarkably conserved. The PFGE DNA fragment size differences in these isolates could be explained to a great extent by differences in the prophage and plasmid contents. Thus, here the nature of variation in different
Salmonella
serovar Typhimurium DT104 isolates is further defined at the gene and whole-genome levels, illustrating how this phage type evolves over time.
The
Mycobacterium avium
Complex
gtfTB
Gene Encodes a Glucosyltransferase Required for the Biosynthesis of Serovar 8-Specific Glycopeptidolipid
Authors: Miyamoto Yuji , Mukai Tetsu , Maeda Yumi , Kai Masanori , Naka Takashi , Yano Ikuya , Makino Masahiko
Published: October 2008

Mycobacterium avium
complex (MAC) is one of the most common opportunistic pathogens widely distributed in the natural environment. The 28 serovars of MAC are defined by variable oligosaccharide portions of glycopeptidolipids (GPLs) that are abundant on the surface of the cell envelope. These GPLs are also known to contribute to the virulence of MAC. Serovar 8 is one of the dominant serovars isolated from AIDS patients, but the biosynthesis of serovar 8-specific GPL remains unknown. To clarify this, we compared gene clusters involved in the biosynthesis of several serovar-specific GPLs and identified the genomic region predicted to be responsible for GPL biosynthesis in a serovar 8 strain. Sequencing of this region revealed the presence of four open reading frames, three unnamed genes and
gtfTB
, the function of which has not been elucidated. The simultaneous expression of
gtfTB
and two downstream genes in a recombinant
Mycobacterium smegmatis
strain genetically modified to produce serovar 1-specific GPL resulted in the appearance of 4,6-
O
-(1-carboxyethylidene)-3-
O
-methyl-glucose, which is unique to serovar 8-specific GPL, suggesting that these three genes participate in its biosynthesis. Furthermore, functional analyses of
gtfTB
indicated that it encodes a glucosyltransferase that transfers a glucose residue via 1→3 linkage to a rhamnose residue of serovar 1-specific GPL, which is critical to the formation of the oligosaccharide portion of serovar 8-specific GPL. Our findings might provide a clue to understanding the biosynthetic regulation that modulates the biological functions of GPLs in MAC.
DNA Repair of 8-Oxo-7,8-Dihydroguanine Lesions in
Porphyromonas gingivalis
Authors: Henry Leroy G. , Sandberg Lawrence , Zhang Kangling , Fletcher Hansel M.
Published: October 2008

The persistence of
Porphyromonas gingivalis
in the inflammatory environment of the periodontal pocket requires an ability to overcome oxidative stress. DNA damage is a major consequence of oxidative stress. Unlike the case for other organisms, our previous report suggests a role for a non-base excision repair mechanism for the removal of 8-oxo-7,8-dihydroguanine (8-oxo-G) in
P. gingivalis
. Because the
uvrB
gene is known to be important in nucleotide excision repair, the role of this gene in the repair of oxidative stress-induced DNA damage was investigated. A 3.1-kb fragment containing the
uvrB
gene was PCR amplified from the chromosomal DNA of
P. gingivalis
W83. This gene was insertionally inactivated using the
ermF-ermAM
antibiotic cassette and used to create a
uvrB
-deficient mutant by allelic exchange. When plated on brucella blood agar, the mutant strain, designated
P. gingivalis
FLL144, was similar in black pigmentation and beta-hemolysis to the parent strain. In addition,
P. gingivalis
FLL144 demonstrated no significant difference in growth rate, proteolytic activity, or sensitivity to hydrogen peroxide from that of the parent strain. However, in contrast to the wild type,
P. gingivalis
FLL144 was significantly sensitive to UV irradiation. The enzymatic removal of 8-oxo-G from duplex DNA was unaffected by the inactivation of the
uvrB
gene. DNA affinity fractionation identified unique proteins that preferentially bound to the oligonucleotide fragment carrying the 8-oxo-G lesion. Collectively, these results suggest that the repair of oxidative stress-induced DNA damage involving 8-oxo-G may occur by a still undescribed mechanism in
P. gingivalis
.
The
hpx
Genetic System for Hypoxanthine Assimilation as a Nitrogen Source in
Klebsiella pneumoniae
: Gene Organization and Transcriptional Regulation
Authors: de la Riva Lucia , Badia Josefa , Aguilar Juan , Bender Robert A. , Baldoma Laura
Published: October 2008

Growth experiments showed that adenine and hypoxanthine can be used as nitrogen sources by several strains of
K. pneumoniae
under aerobic conditions. The assimilation of all nitrogens from these purines indicates that the catabolic pathway is complete and proceeds past allantoin. Here we identify the genetic system responsible for the oxidation of hypoxanthine to allantoin in
K. pneumoniae.
The
hpx
cluster consists of seven genes, for which an organization in four transcriptional units,
hpxDE
,
hpxR
,
hpxO
, and
hpxPQT
, is proposed. The proteins involved in the oxidation of hypoxanthine (HpxDE) or uric acid (HpxO) did not display any similarity to other reported enzymes known to catalyze these reactions but instead are similar to oxygenases acting on aromatic compounds. Expression of the
hpx
system is activated by nitrogen limitation and by the presence of specific substrates, with
hpxDE
and
hpxPQT
controlled by both signals. Nitrogen control of
hpxPQT
transcription, which depends on σ
54
, is mediated by the Ntr system. In contrast, neither NtrC nor the nitrogen assimilation control protein is involved in the nitrogen control of
hpxDE
, which is dependent on σ
70
for transcription. Activation of these operons by the specific substrates is also mediated by different effectors and regulatory proteins. Induction of
hpxPQT
requires uric acid formation, whereas expression of
hpxDE
is induced by the presence of hypoxanthine through the regulatory protein HpxR. This LysR-type regulator binds to a TCTGC-N
4
-GCAAA site in the intergenic
hpxD-hpxR
region. When bound to this site for
hpxDE
activation, HpxR negatively controls its own transcription.
Genetic Adaptation of
Pseudomonas aeruginosa
to the Airways of Cystic Fibrosis Patients Is Catalyzed by Hypermutation
Authors: Mena A. , Smith E. E. , Burns J. L. , Speert D. P. , Moskowitz S. M. , Perez J. L. , Oliver A.
Published: October 2008

In previous work (E. E. Smith, D. G. Buckley, Z. Wu, C. Saenphimmachack, L. R. Hoffman, D. A. D'Argenio, S. I. Miller, B. W. Ramsey, D. P. Speert, S. M. Moskowitz, J. L. Burns, R. Kaul, and M. V. Olson, Proc. Natl. Acad. Sci. USA
103:
8487-8492, 2006) it was shown that
Pseudomonas aeruginosa
undergoes intense genetic adaptation during chronic respiratory infection (CRI) in cystic fibrosis (CF) patients. We used the same collection of isolates to explore the role of hypermutation in this process, since one of the hallmarks of CRI is the high prevalence of DNA mismatch repair (MMR) system-deficient mutator strains. The presence of mutations in 34 genes (many of them positively linked to adaptation in CF patients) in the study collection of 90
P. aeruginosa
isolates obtained longitudinally from 29 CF patients was not homogeneous; on the contrary, mutations were significantly concentrated in the mutator lineages, which represented 17% of the isolates (87% MMR deficient). While sequential nonmutator lineages acquired a median of only 0.25 mutation per year of infection, mutator lineages accumulated more than 3 mutations per year. On the whole-genome scale, data for the first fully sequenced late CF isolate, which was also shown to be an MMR-deficient mutator, also support these findings. Moreover, for the first time the predicted amplification of mutator populations due to hitchhiking with adaptive mutations in the course of natural human infections is clearly documented. Interestingly, increased accumulation of mutations in mutator lineages was not a consequence of overrepresentation of mutations in genes involved in antimicrobial resistance, the only adaptive trait linked so far to hypermutation in CF patients, demonstrating that hypermutation also plays a major role in
P. aeruginosa
genome evolution and adaptation during CRI.
Extended-Spectrum Beta-Lactamase Detection with Different Panels for Automated Susceptibility Testing and with a Chromogenic Medium
Authors: Färber J. , Moder K.-A. , Layer F. , Tammer I. , König W. , König B.
Published: October 2008

Infections caused by extended-spectrum beta-lactamase (ESBL)- and
ampC
beta-lactamase-producing gram-negative bacteria complicate therapy and limit treatment options. Several different panels for ESBL detection with automated systems exist. In addition, a chromogenic agar medium is available for ESBL screening. We compared two automated identification and susceptibility testing systems with regard to their effectiveness in detecting ESBL production in
Enterobacteriaceae
: the BD Phoenix system (BD Diagnostic Systems, Sparks, MD) and the Vitek 2 system (bioMerieux, Marcy l'Etoile, France). We tested 114 strains using the Etest as the standard, various available panels for both automated systems (for BD Phoenix, the NMIC/ID-50 and NMIC/ID-70 GN Combo panels for combined identification and susceptibility testing of gram-negative bacilli, and for Vitek 2, the ID-GNB panel for identification of gram-negative bacilli and the AST-N020, AST-N041, and AST-N062 panels for susceptibility testing), and a chromogenic agar medium (bioMérieux, Marcy l'Etoile, France). PCR for common ESBL gene families (encoding TEM, SHV, OXA, and CTX-M) and for chromosomal or plasmid-mediated
ampC
beta-lactamase genes was conducted to complete the study design. For the tested specimens overall, the chromID ESBL agar showed the highest sensitivity (95.8%) but the lowest specificity (10.5%) compared to the sensitivity and specificity of the Etest (chosen as reference by the authors) for the detection of ESBL-producing strains. The BD Phoenix system showed sensitivities of 77.1% and 84.2% and specificities of 61.5% and 75.0%, respectively, for the NMIC/ID-50 andNMIC/ID-70 panels. The sensitivity of the Vitek 2 system ranged from 78.8% (AST-N020) to 80.6% (AST-N062) and up to 84.2% (AST-N041). The specificities of the respective panels were 50.0% (AST-N041 and AST-N062) and 55.6% (AST-N020). In conclusion, the sensitivities and specificities of ESBL detection by the different methods differ depending on the microorganisms under study.
Evaluation of Repeat
Clostridium difficile
Enzyme Immunoassay Testing
Authors: Cardona Diana M. , Rand Kenneth H.
Published: October 2008

Clostridium difficile
is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis, which have significant morbidity and mortality. Accurate and timely diagnosis is critical. Repeat enzyme immunoassay testing for
C. difficile
toxin has been recommended because of <100% sensitivity. All
C. difficile
tests between 1 January 2006 and 31 December 2006 were retrospectively analyzed for results and testing patterns. The Wampole
C. difficile
Tox A/B II enzyme immunoassay kit was used. There were a total of 8,256 tests from 3,112 patients; 49% of tests were repeated. Of the 3,749 initially negative patient tests, 96 were positive upon repeat testing within 10 days of the first test. Of repeat tests, 0.9% repeated on day 0 (same day as the first test), 1.8% on day 1, 3.8% on day 2, 2.6% on day 3, 5.4% on days 4 to 6, and 10.6% on days 7 to 10 were positive. Thirty-eight patients had a positive test within 48 h of an initial negative test, and based on chart review, 18 patients were treated empirically while 16 were treated following the new result. None had evidence of medical complications. Of initially positive patients, 91% were positive upon repeat testing on day 0, 75% on day 1, and 58% on day 2, to a low of 14% on days 7 to 10. Depending on the clinical setting, these data support not repeating
C. difficile
tests within 2 days of a negative result and limiting repeat testing to ≥1 week of a positive result.
Detection of CirculatingAspergillus fumigatusDNA by Real-Time PCR Assay of Large Serum Volumes Improves Early Diagnosis of Invasive Aspergillosis in High-Risk Adult Patients under Hematologic Surveillance
Authors: Suarez F. , Lortholary O. , Buland S. , Rubio M. T. , Ghez D. , Mahé V. , Quesne G. , Poirée S. , Buzyn A. , Varet B. , Berche P. , Bougnoux M. E.
Published: October 2008

Detection of galactomannan antigen (GMA) in serum is the standard assay for the diagnosis of invasive aspergillosis (IA) in high-risk patients with hematological disorders. Detection ofAspergillusDNA in serum has been proposed, but its sensitivity is lower than that of GMA when small serum volumes (SSV) are used. In this study, we investigated whether extraction of DNA from large serum volumes (LSV) improves diagnostic yield. In a 13-month prospective study, we compared the performances of twice-weekly screening of serum for GMA by an enzyme immunoassay and weekly screening forAspergillus fumigatusDNA by a real-time PCR (RT-PCR) assay of 1.0 ml (LSV) or 100 μl (SSV) of serum. We included 124 patients (138 treatment episodes), with 17 episodes of EORTC (European Organization for Research and Treatment of Cancer)/MSG (Mycoses Study Group)-documented IA. In all, 1,870 samples were screened for GMA. The sensitivity (Se), specificity (Sp), and positive and negative predictive values (PPV and NPV, respectively) of GMA for IA were 88.2%, 95.8%, 75%, and 98.3%, respectively. We screened 938 samples forAspergillusDNA by using LSV; 404 of these samples were also tested with SSV. The Se, Sp, PPV, and NPV of RT-PCR were 100%, 96.7%, 81%, and 100%, respectively, with LSV and 76.5%, 96.7%, 81.3%, and 95.6%, respectively, with SSV. DNA detection gave a positive result when performed on LSV in two cases of IA where the GMA assay result remained negative. Furthermore, in four IA cases, DNA was detected earlier than GMA. The use of LSV for extraction improved the performance of the RT-PCR, which appears highly sensitive and specific for the early diagnosis of IA in high-risk patients with hematological disorders.
New Insights into Prevalence, Genetic Diversity, and Proviral Load of Human T-Cell Leukemia Virus Types 1 and 2 in Pregnant Women in Gabon in Equatorial Central Africa
Authors: Etenna Sonia Lekana-Douki , Caron Mélanie , Besson Guillaume , Makuwa Maria , Gessain Antoine , Mahé Antoine , Kazanji Mirdad
Published: October 2008

Human T-cell leukemia virus type 1 (HTLV-1) is highly endemic in areas of central Africa; mother-to-child transmission and sexual transmission are considered to be the predominant routes. To determine the prevalence and subtypes of HTLV-1/2 in pregnant women in Gabon, we conducted an epidemiological survey in the five main cities of the country. In 907 samples, the HTLV-1 seroprevalence was 2.1%, which is lower than that previously reported. Only one case of HTLV-2 infection was found. The HTLV-1 seroprevalence increased with age and differed between regions (
P
≤ 0.05), with the highest prevalence (5%) in the southeastern region. A wide range of HTLV-1 proviral loads was observed among the infected women. The level of the proviral load was correlated with a high HTLV-1 antibody titer (
P
≤ 0.02). Sequencing of HTLV-1
env
and long terminal repeat fragments showed that all but one strain belonged to the central African subtype B; the outlier was of cosmopolitan subtype A. The new strains of subtype B exhibited wide genetic diversity, but there was no evidence of clustering of specific genomes within geographical regions of the country. Some strains were closely related to simian T-cell leukemia virus type 1 strains of great apes, suggesting that in these areas some HTLV-1 strains could arise from relatively recent interspecies transmission. The sole HTLV-2 strain belonged to subtype B. In this study we showed that the prevalence of HTLV-1 in the southeast is one of the highest in the world for pregnant women.
“Working to shape what society’s expectations of us should be”: Philip Morris’ societal alignment strategy
Authors: Yang J S , Malone R E
Published: October 2008

Background:

A key element of Philip Morris’s (PM’s) corporate social responsibility initiatives is “societal alignment”, defined as “strategies and programs to meet society’s expectations of a responsible tobacco company”. This study explored the genesis and implementation of Philip Morris' (PM) societal alignment efforts.

Methods:

The study retrieved and analysed approximately 375 previously undisclosed PM documents now available electronically. Using an iterative process, the study categorised themes and prepared a case analysis.

Results:

Beginning in 1999, PM sought to become “societally aligned” by identifying expectations of a responsible tobacco company through public opinion research and developing and publicising programs to meet those expectations. Societal alignment was undertaken within the US and globally to ensure an environment favourable to PM’s business objectives. Despite PM’s claims to be “changing”, however, societal alignment in practice was highly selective. PM responded to public “expectations” largely by retooling existing positions and programs, while entirely ignoring other expectations that might have interfered with its business goals. It also appears that convincing employees of the value and authenticity of societal alignment was difficult.

Conclusions:

As implementation of the Framework Convention on Tobacco Control proceeds, tobacco control advocates should closely monitor development of such “alignment” initiatives and expose the motivations and contradictions they reveal.
Behavior in tissue culture of nitrogen-fixing root nodules of Ceanothus integerrimus
Authors: Ellmore George S. , Strand Ruth , Laetsch W. M.
Published: October 2008

This study documents the in vitro growth of N2-fixing root nodules from the dicotyledonous shrub Ceanothus integerrimus (Rhamnaceae). Root nodule lobes were removed from cultivated plants, surface sterilized, and cultured on agar media containing varied amounts of nitrogen (N). Uninfected cells inside the cultured nodules divide and form a callus which is visible after 7 days of growth. Cells infected by the N2-fixing actinomycete do not divide, but rather degenerate. Host cell cytoplasm disappears and organelles and the plasma membrane are no longer seen under the electron microscope. Endophyte structure also deteriorates. Nucleoid areas within the terminal vesicles become diffuse. Cross walls separating vesicles from the hyphae disappear and cytoplasm of the hyphae withdraws from the actinomycete wall. Ceanothus nodules readily form callus in tissue culture. Callus proliferates from uninfected cortical parenchyma outside the infection zone. The callus is free of living endophyte and is incapable of fixing N2 as measured by acetylene reduction. Nodule tissue growth in vitro is more vigorous on media with high N than on N-deficient media.
Morphogenesis of conidiomata in Chaetomella acutiseta (Coelomycetes)
Authors: DiCosmo Frank , Cole Garry T.
Published: October 2008

Developmental and ultrastructural aspects of conidiomata (pycnidia) in Chaetomella acutiseta var. acutiseta were examined in pure culture and on sterile oak leaves. The earliest recognized sign of pycnidial formation in this fungus is the aggregation of hyphae at the base of an erect seta. Subsequently, the hyphae adjacent to the seta become intermingled and then orient themselves parallel to one another as they rise up from the surface of the substrate. Additional setae form about the perimeter of the young pycnidium. Ontogenetic features of the cavity of conidiomata were examined by cryo-sectioning. As the pycnidium enlarges, the internal hyphae become more loosely packed and then differentiate into conidiophores bearing phialides.