bluuebunny/crossref_metadata_2025 huggingface dataset:
Acoustic measurement of the
Deepwater Horizon
Macondo well flow rate
Authors: Camilli Richard , Di Iorio Daniela , Bowen Andrew , Reddy Christopher M. , Techet Alexandra H. , Yoerger Dana R. , Whitcomb Louis L. , Seewald Jeffrey S. , Sylva Sean P. , Fenwick Judith
Published: September 2011

On May 31, 2010, a direct acoustic measurement method was used to quantify fluid leakage rate from the
Deepwater Horizon
Macondo well prior to removal of its broken riser. This method utilized an acoustic imaging sonar and acoustic Doppler sonar operating onboard a remotely operated vehicle for noncontact measurement of flow cross-section and velocity from the well’s two leak sites. Over 2,500 sonar cross-sections and over 85,000 Doppler velocity measurements were recorded during the acquisition process. These data were then applied to turbulent jet and plume flow models to account for entrained water and calculate a combined hydrocarbon flow rate from the two leak sites at seafloor conditions. Based on the chemical composition of end-member samples collected from within the well, this bulk volumetric rate was then normalized to account for contributions from gases and condensates at initial leak source conditions. Results from this investigation indicate that on May 31, 2010, the well’s oil flow rate was approximately 0.10 ± 0.017 m
3
 s
-1
at seafloor conditions, or approximately 85 ± 15 kg s
-1
(7.4 ± 1.3 Gg d
-1
), equivalent to approximately 57,000 ± 9,800 barrels of oil per day at surface conditions. End-member chemical composition indicates that this oil release rate was accompanied by approximately an additional 24 ± 4.2 kg s
-1
(2.1 ± 0.37 Gg d
-1
) of natural gas (methane through pentanes), yielding a total hydrocarbon release rate of 110 ± 19 kg s
-1
(9.5 ± 1.6 Gg d
-1
).
Myeloid-specific estrogen receptor α deficiency impairs metabolic homeostasis and accelerates atherosclerotic lesion development
Authors: Ribas Vicent , Drew Brian G. , Le Jamie A. , Soleymani Teo , Daraei Pedram , Sitz Daniel , Mohammad Laila , Henstridge Darren C. , Febbraio Mark A. , Hewitt Sylvia C. , Korach Kenneth S. , Bensinger Steven J. , Hevener Andrea L.
Published: September 2011

ERα is expressed in macrophages and other immune cells known to exert dramatic effects on glucose homeostasis. We investigated the impact of ERα expression on macrophage function to determine whether hematopoietic or myeloid-specific ERα deletion manifests obesity-induced insulin resistance in mice. Indeed, altered plasma adipokine and cytokine levels, glucose intolerance, insulin resistance, and increased adipose tissue mass were observed in animals harboring a hematopoietic or myeloid-specific deletion of ERα. A similar obese phenotype and increased atherosclerotic lesion area was displayed in LDL receptor-KO mice transplanted with ERα
−/−
bone marrow. In isolated macrophages, ERα was necessary for repression of inflammation, maintenance of oxidative metabolism, IL-4–mediated induction of alternative activation, full phagocytic capacity in response to LPS, and oxidized LDL-induced expression of ApoE and Abca1. Furthermore, we identified ERα as a direct regulator of macrophage transglutaminase 2 expression, a multifunctional atheroprotective enzyme. Our findings suggest that diminished ERα expression in hematopoietic/myeloid cells promotes aspects of the metabolic syndrome and accelerates atherosclerosis in female mice.
Affinity maturation of human CD4 by yeast surface display and crystal structure of a CD4–HLA-DR1 complex
Authors: Wang Xin Xiang , Li Yili , Yin Yiyuan , Mo Min , Wang Qian , Gao Wei , Wang Lili , Mariuzza Roy A.
Published: September 2011

Helper T-cell activation generally requires the coreceptor CD4, which binds MHC class II molecules. A remarkable feature of the CD4–MHC class II interaction is its exceptionally low affinity, which ranges from
K
D
= ∼200 μM to >2 mM. Investigating the biological role of the much lower affinity of this interaction than those of other cell–cell recognition molecules will require CD4 mutants with enhanced binding to MHC class II for testing in models of T-cell development. To this end, we used in vitro-directed evolution to increase the affinity of human CD4 for HLA-DR1. A mutant CD4 library was displayed on the surface of yeast and selected using HLA-DR1 tetramers or monomers, resulting in isolation of a CD4 clone containing 11 mutations. Reversion mutagenesis showed that most of the affinity increase derived from just two substitutions, Gln40Tyr and Thr45Trp. A CD4 variant bearing these mutations bound HLA-DR1 with
K
D
= 8.8 μM, compared with >400 μM for wild-type CD4. To understand the basis for improved affinity, we determined the structure of this CD4 variant in complex with HLA-DR1 to 2.4 Å resolution. The structure provides an atomic-level description of the CD4-binding site on MHC class II and reveals how CD4 recognizes highly polymorphic HLA-DR, -DP, and -DQ molecules by targeting invariant residues in their α2 and β2 domains. In addition, the CD4 mutants reported here constitute unique tools for probing the influence of CD4 affinity on T-cell activation and development.
Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids
Authors: Zhou Renchao , Moshgabadi Noushin , Adams Keith L.
Published: September 2011

Polyploidy has been a common process during the evolution of eukaryotes, especially plants, leading to speciation and the evolution of new gene functions. Gene expression levels and patterns can change, and gene silencing can occur in allopolyploids—phenomena sometimes referred to as “transcriptome shock.” Alternative splicing (AS) creates multiple mature mRNAs from a single type of precursor mRNA. Here we examined the evolution of AS patterns after polyploidy, with natural and two resynthesized allotetraploid
Brassica napus
lines, using RT-PCR and sequencing assays of 82 AS events in duplicated gene pairs (homeologs). Comparing the AS patterns between the two homeologs in natural
B. napus
revealed that many of the gene pairs show different AS patterns, with a few showing variation that was organ specific or induced by abiotic stress treatments. In the resynthesized allotetraploids, 26–30% of the duplicated genes showed changes in AS compared with the parents, including many cases of AS event loss after polyploidy. Parallel losses of many AS events after allopolyploidy were detected in the two independently resynthesized lines. More changes occurred in parallel between the two lines than changes specific to each line. The
PASTICCINO
gene showed partitioning of two AS events between the two homeologs in the resynthesized allopolyploids. AS changes after allopolyploidy were much more common than homeolog silencing. Our findings indicate that AS patterns can change rapidly after polyploidy, that many genes are affected, and that AS changes are an important component of the transcriptome shock experienced by new allopolyploids.
Iconic gesture and speech integration in younger and older adults
Authors: Cocks Naomi , Morgan Gary , Kita Sotaro
Published: September 2011

This study investigated the impact of age on iconic gesture and speech integration. The performance of a group of older adults (60–76 years) and a group of younger adults (22–30 years) were compared on a task which required the comprehension of information presented in 3 different conditions: verbal only, gesture only, and verbal and gesture combined. The older adults in the study did not benefit as much from multi-modal input as the younger adults and were more likely to ignore gesture when decoding the multi-modal information.
Cognitive skills and gesture–speech redundancy
Authors: Hostetter Autumn B. , Alibali Martha W.
Published: September 2011

Speakers sometimes convey information in their gestures that they do not convey in the accompanying speech. The present study examined whether individual differences in the production of non-redundant gesture–speech combinations are related to individual differences in speakers’ spatial and verbal skills. We classified speakers as spatial dominant, verbal dominant, or equally matched on the basis of the difference in their performance on a spatial visualization test and a verbal fluency test. We used the coding procedure developed by Alibali et al. (2009) to code speakers’ gesture–speech redundancy as they narrated an animated cartoon. Spatial-dominant speakers produced a higher proportion of non-redundant gesture–speech combinations than other speakers. The results suggest that some speakers may use non-redundant gesture–speech combinations as a communicative strategy that enables them to capitalize on their strong imagistic representations.
Training
Authors: Cattanach Ann
Published: September 2011

This section is for people to report on courses they have attended or for trainers/colleges etc. to describe their courses/syllabuses at some depth.
When I Am an Old Woman…. Using Dramatherapy as a Treatment for Depression with Functional Elderly People
Authors: Reinstein Mike
Published: September 2011

When I am an old woman I shall wear purple With a red hat which doesn't go and doesn't suit me (Jenny Joseph)
Children's Response to War as Represented in Their Narratives
Authors: Feniger-Schaal Rinat
Published: September 2011

This present study aimed to examine the impact of the experience of war on children's mental representations, with a particular focus on parental and self-representation and affect regulation. 32 children age 6–8 were assessed using a narrative technique together with behaviour reports, comparing some of the data with children from a non-war environment. Aggression, anxiety, hyper-vigilance, increased sensitivity, and possible influence on attachment representations were expected to be present in the narratives of children exposed to war. The expectation for these themes is explained using Anna Freud's ideas about aggression and anxiety, the literature linking child maltreatment and affect regulation, Cicchetti's model that explains the link to the child maltreatment literature, and Bowlby's ideas about parents and self-representations.
The Hunter's Son
Authors: Stolfi Daniel
Published: September 2011

THE AWESOME PUPPET COMPANY recently performed its first outing of The Hunter's Son, an adaptation of a West African Hausa dilemma tale, The Tale of a Hunter and his Son,1 as part of a psychotherapy weekend retreat.2 The performance was devised as a blueprint for using puppetry therapeutically in men's work, from which a range of individual and group clinical spin-offs can be rolled out for different male client needs, including father-son relationships; personal-public leadership and social role identities; war trauma; substance abuse and rehabilitation; and other significant therapeutic explorations of restorative and reparative behaviour practice. The project was also a prototype for enlisting student placement work and Paula Andreewitch, final year drama at Bristol University (2009), contributed significantly sharing production, design and execution. As therapeutic puppetry generally remains fairly underutilized, the session afforded a valuable opportunity to explore how the medium might be used as a significant Dramatherapeutic tool with adult populations. Given the audience's positive response to the performance, I thought it would be of some interest to share a few personal reflections on the project.
Enzymatic degradation of proteinaceous compounds in sediments exposed to intensive mariculture in the tropics
Authors: Reichardt Wolfgang , Bolalin Gerome V. , Cutchon Xerxes D. R. , Que Frances V. J. , Balgos Marie J. T. D.
Published: September 2011

Anoxic and sulfidic sediments formed during intensive milkfish farming in Bolinao Bay (Lingayen Gulf, Luzon, Philippines) showed concentrations of total proteinaceous matter roughly three times higher (up to16.9 mg cm−3) than those of less reduced sediments. Ectoprotease activities in these coastal sediments suggested an inhibition of enzymatic recycling of proteins by sulfide. Sodium sulfide proved capable of inhibiting protease activity produced by a bacterial isolate from a sulfidic sediment site (Ki = 20 mM Na2S · 9H2O). Reoxidation and removal of H2S from sulfidic sediments, however, proved inadequate to recover proteolytic activity. Hence, H2S formed during organic matter mineralization via bacterial sulfate respiration may have initiated an irreversible inhibition of the enzymatic degradation of proteinaceous matter from fish farming. Ectoprotease activity was positively correlated (r = .93) with redox potential values. Lowest proteolytic activities were found in strongly reduced sediments, that were predominantly fine grained (very fine sand and silt) and sulfidic at the same time. Low ectoprotease activity in these sulfide-rich sediments can be interpreted as a kind of negative feedback mechanism that would mitigate the immediate recycling of excessive amounts of feed borne protein-rich deposits. Proteins may be further protected from degradation by selective particle adsorption in the finest grained deposits of fish farming waste.
Dust storms over the Arabian Gulf: a possible indicator of climate changes consequences
Authors: Hamza Waleed , Enan Mohamed Rizk , Al-Hassini Huda , Stuut Jan-Berend , de-Beer Dirk
Published: September 2011

Dust storm frequencies and strengths were monitored during 2009 at various locations along the coast of the United Arab Emirates (UAE), as representative sites of the Arabian Gulf marine environment. The results have been compared with a pre-2009 five-year data set. Mineralogical components of dust samples collected during the 2009 study period were analyzed using both X-ray diffraction (XRD) and X-ray Fluorescence (XRF) techniques. The comparison of the 2009 and pre-2009 data revealed a shift in the characteristics of dust storms in the Arabian Gulf, which may constitute a sensitive indicator of climate change affecting the region. The range of mineral compositions of the collected dust samples is consistent with temporally and spatially variable dust sources, associated with changing wind patterns over the Arabian Gulf. From a positive perspective, the dust may deliver mineralogical nutrients enhancing microbial productivity in the marine ecosystem. Increasing productivity and liberation of iron from sediments will lead to an increase of Dimethyl Sulfide (DMS) in the atmosphere, which by oxidation will scatter solar radiation effectively with a consequent decrease in global temperature as a climate feedback.
Evaluation of small-scale habitat manipulation to reduce the impact of the whirling disease parasite in streams
Authors: Thompson Kevin G.
Published: September 2011

The effects on trout of the whirling disease parasite Myxobolus cerebralis were evaluated to observe whether they could be ameliorated by intervening with physical habitat manipulations. Physical stream habitat was modified at field sites in Spring Creek and Williams Fork River, Colorado, USA to reduce or eliminate habitat for the invertebrate oligochaete host of  M. cerebralis, Tubifex tubifex. Data were collected before and after habitat modifications on total oligochaete and T. tubifex biomass, actinospore production from oligochaete samples, surface water actinospore concentrations, and prevalence and intensity of myxospore development in Brown Trout, Salmo trutta. Oligochaete biomass estimates lacked precision due to inherently patchy distribution of the target organisms. Oligochaetes quickly re-occupied a portion of habitat at the Williams Fork River site, but oligochaete biomass was depressed for nearly a year at the Spring Creek site. All T. tubifex in Spring Creek belonged to a susceptible lineage, but in the Williams Fork River there was a mix of susceptible and non-susceptible T. tubifex. Actinospore detection in filtered surface water samples showed consistent but minor reduction in density in Williams Fork River and no difference or even higher densities in Spring Creek after habitat modification. Myxospore prevalence and intensity of infection in Brown Trout appeared to decrease in Williams Fork River after habitat modification, but there is evidence that a similar decrease also occurred at a control site in that stream. Spring Creek showed no effect for these metrics. The differing responses may have been influenced by T. tubifex lineage differences. The habitat manipulations did not show sufficient promise to encourage further efforts in Colorado.
Identification of coastal water quality by self-organizing map in Sanya Bay, South China Sea
Authors: Wu Mei-Lin , Zhang Yan-Ying , Dong Jun-De , Wang You-Shao , Cai Chuang-Hua
Published: September 2011

A self-organizing map (SOM) was utilized to identify the effects caused by human activities on water quality in Sanya Bay, South China Sea. Spatial pattern is mainly related to anthropogenic activities and hydrodynamic conditions. Water quality in Sanya Bay was divided into two groups by SOM: S1 and S2 were in east parts of Sanya Bay (Sanya River Estuary), which are areas of human activity, while the rest of the monitoring sites were in the south, central and northern parts of Sanya Bay, which are areas that have water exchanges from South China Sea. The results of this study may provide information on spatial patterns in Sanya Bay.
Spin-transfer torque induced vortex dynamics in Fe/Ag/Fe nanopillars
Authors: Sluka V , Kákay A , Deac A M , Bürgler D E , Hertel R , Schneider C M
Published: September 2011

We report on the experimental and analytical work on spin-transfer torque induced vortex dynamics in metallic nanopillars with in-plane magnetized layers. We study nanopillars with a diameter of 150 nm, containing two Fe layers with a thickness of 15 nm and 30 nm, respectively, separated by a 6 nm Ag spacer. The sample geometry is such that it allows for the formation of magnetic vortices in the Fe discs. As confirmed by micromagnetic simulations, we are able to prepare states where one magnetic layer is homogeneously magnetized while the other contains a vortex. We experimentally show that in this configuration spin-transfer torque can excite vortex dynamics and analyse their dependence on a magnetic field applied in the sample plane. The centre of gyration is continuously dislocated from the disc centre, and the potential changes its shape with field strength. The latter is reflected in the field dependence of the excitation frequency. In the second part we propose a novel mechanism for the excitation of the gyrotropic mode in nanopillars with a perfectly homogeneously magnetized in-plane polarizing layer. We analytically show that in this configuration the vortex can absorb energy from the spin-polarized electric current if the angular spin-transfer efficiency function is asymmetric. This effect is supported by micromagnetic simulations.
The effect of processing conditions on the structural morphology and physical properties of ZnO and CdS thin films produced via sol–gel synthesis and chemical bath deposition techniques
Authors: Salam Shahzad , Islam Mohammad , Alam Mahboob , Akram Aftab , Ikram Mujtaba , Mahmood Asif , Khan Majid , Mujahid Mohammad
Published: September 2011

Cadmium sulfide (CdS) and zinc oxide (ZnO) are used in thin film solar cells as buffer layer and transparent conducting oxide, respectively. The effect of annealing conditions on the morphology and physical properties of CdS and ZnO films prepared using chemical bath deposition and sol–gel synthesis techniques, respectively, was investigated. CdS films obtained from the chemical bath deposition (CBD) process were found to be polycrystalline with dense granular morphology. Electrical characterization of the films annealed at 400 °C for 10 min yielded values of 2.2×10−3 Ω cm and 8.3×1012 
cm
−3 for resistivity and carrier concentration, respectively. Scanning electron microscopy (SEM) and x-ray diffraction (XRD) studies of intrinsic zinc oxide (i-ZnO) films revealed flake-like morphology and transformation of the as-deposited amorphous structure into a hexagonal wurtzite crystal structure upon annealing at 500 °C for 2 h. Optical and electrical characterization results showed that such films had ∼80% transmittance and resistivity values as low as 6.4×102 Ω cm. These films are being explored for fabrication and testing of copper-indium-gallium-(di)selenide (CIGS) thin film solar cells obtained from simple, cost-effective, solution-based synthesis routes.
Qualitative properties of solutions to a time-space fractional evolution equation
Authors: Fino Ahmad , Kirane Mokhtar
Published: September 2011

In this article, we analyze a spatio-temporally nonlocal nonlinear parabolic equation. First, we validate the equation by an existence-uniqueness result. Then, we show that blowing-up solutions exist and study their time blow-up profile. Also, a result on the existence of global solutions is presented. Furthermore, we establish necessary conditions for local or global existence.
Membrane-targeted WAVE mediates photoreceptor axon targeting in the absence of the WAVE complex inDrosophila
Authors: Stephan Raiko , Gohl Christina , Fleige Astrid , Klämbt Christian , Bogdan Sven
Published: September 2011

A tight spatial-temporal coordination of F-actin dynamics is crucial for a large variety of cellular processes that shape cells. The Abelson interactor (Abi) has a conserved role in Arp2/3-dependent actin polymerization, regulating Wiskott-Aldrich syndrome protein (WASP) and WASP family verprolin-homologous protein (WAVE). In this paper, we report that Abi exerts nonautonomous control of photoreceptor axon targeting in the Drosophila visual system through WAVE. In abi mutants, WAVE is unstable but restored by reexpression of Abi, confirming that Abi controls the integrity of the WAVE complex in vivo. Remarkably, expression of a membrane-tethered WAVE protein rescues the axonal projection defects of abi mutants in the absence of the other subunits of the WAVE complex, whereas cytoplasmic WAVE only slightly affects the abi mutant phenotype. Thus complex formation not only stabilizes WAVE, but also provides further membrane-recruiting signals, resulting in an activation of WAVE.
Munc18-1 domain-1 controls vesicle docking and secretion by interacting with syntaxin-1 and chaperoning it to the plasma membrane
Authors: Han Gayoung A. , Malintan Nancy T. , Saw Ner Mu Nar , Li Lijun , Han Liping , Meunier Frederic A. , Collins Brett M. , Sugita Shuzo
Published: September 2011

Munc18-1 plays pleiotropic roles in neurosecretion by acting as 1) a molecular chaperone of syntaxin-1, 2) a mediator of dense-core vesicle docking, and 3) a priming factor for soluble N-ethylmaleimide–sensitive factor attachment protein receptor–mediated membrane fusion. However, how these functions are executed and whether they are correlated remains unclear. Here we analyzed the role of the domain-1 cleft of Munc18-1 by measuring the abilities of various mutants (D34N, D34N/M38V, K46E, E59K, K46E/E59K, K63E, and E66A) to bind and chaperone syntaxin-1 and to restore the docking and secretion of dense-core vesicles in Munc18-1/-2 double-knockdown cells. We identified striking correlations between the abilities of these mutants to bind and chaperone syntaxin-1 with their ability to restore vesicle docking and secretion. These results suggest that the domain-1 cleft of Munc18-1 is essential for binding to syntaxin-1 and thereby critical for its chaperoning, docking, and secretory functions. Our results demonstrate that the effect of the alleged priming mutants (E59K, D34N/M38V) on exocytosis can largely be explained by their reduced syntaxin-1–chaperoning functions. Finally, our data suggest that the intracellular expression and distribution of syntaxin-1 determines the level of dense-core vesicle docking.
The filament-forming protein Pil1 assembles linear eisosomes in fission yeast
Authors: Kabeche Ruth , Baldissard Suzanne , Hammond John , Howard Louisa , Moseley James B.
Published: September 2011

The cortical cytoskeleton mediates a range of cellular activities such as endocytosis, cell motility, and the maintenance of cell rigidity. Traditional polymers, including actin, microtubules, and septins, contribute to the cortical cytoskeleton, but additional filament systems may also exist. In yeast cells, cortical structures called eisosomes generate specialized domains termed MCCs to cluster specific proteins at sites of membrane invaginations. Here we show that the core eisosome protein Pil1 forms linear cortical filaments in fission yeast cells and that purified Pil1 assembles into filaments in vitro. In cells, Pil1 cortical filaments are excluded from regions of cell growth and are independent of the actin and microtubule cytoskeletons. Pil1 filaments assemble slowly at the cell cortex and appear stable by time-lapse microscopy and fluorescence recovery after photobleaching. This stability does not require the cell wall, but Pil1 and the transmembrane protein Fhn1 colocalize and are interdependent for localization to cortical filaments. Increased Pil1 expression leads to cytoplasmic Pil1 rods that are stable and span the length of cylindrical fission yeast cells. We propose that Pil1 is a novel component of the yeast cytoskeleton, with implications for the role of filament assembly in the spatial organization of cells.
Dual regulatory pathways of flagellar gene expression by ClpXP protease in enterohaemorrhagic Escherichia coli
Authors: Kitagawa Ryo , Takaya Akiko , Yamamoto Tomoko
Published: September 2011

In enterobacteria such asEscherichia coliandSalmonellaspecies, flagellar biogenesis is strictly dependent upon the master regulatorflhDC. Here, we demonstrate that in enterohaemorrhagicE. coli(EHEC), the flagellar regulon is controlled by ClpXP, a member of the ATP-dependent protease family, through two pathways: (i) post-translational control of the FlhD/FlhC master regulator and (ii) transcriptional control of theflhDCoperon. Both FlhD and FlhC proteins accumulated markedly following ClpXP depletion, and their half-lives were significantly longer in the mutant cells, suggesting that ClpXP is responsible for degrading FlhD and FlhC proteins, leading to downregulation of flagellar expression. ClpXP was involved in regulating the transcription of theflhDpromoter only when the cells had entered stationary phase in a culture medium that markedly induced expression of the locus of enterocyte effacement (LEE). Comparative analyses of transcription from theflhDpromoter in EHEC cells with different genetic backgrounds suggested that the downregulation offlhDCexpression by ClpXP is dependent on the LEE-encoded GrlR–GrlA system. We have also shown that the degradation of FlhD and FlhC by ClpXP is responsible for downregulating flagellar expression even when LEE expression is induced.
The glgB-encoded glycogen branching enzyme is essential for glycogen accumulation in Corynebacterium glutamicum
Authors: Seibold Gerd M. , Breitinger Katrin J. , Kempkes Raoul , Both Leonard , Krämer Matthias , Dempf Stefan , Eikmanns Bernhard J.
Published: September 2011

Corynebacterium glutamicum transiently accumulates glycogen as carbon capacitor during the early exponential growth phase in media containing carbohydrates. In some bacteria glycogen is synthesized by the consecutive action of ADP-glucose pyrophosphorylase (GlgC), glycogen synthase (GlgA) and glycogen branching enzyme (GlgB). GlgC and GlgA of C. glutamicum have been shown to be necessary for glycogen accumulation in this organism. However, although cg1381 has been annotated as the putative C. glutamicum glgB gene, cg1381 and its gene product have not been characterized and their role in transient glycogen accumulation has not yet been investigated. We show here that the cg1381 gene product of C. glutamicum catalyses the formation of α-1,6-glycosidic bonds in polysaccharides and thus represents a glycogen branching enzyme. RT-PCR experiments revealed glgB to be co-transcribed with glgE, probably encoding a maltosyltransferase. Promoter activity assays with the glgE promoter region revealed carbon-source-dependent expression of the glgEB operon. Characterization of the growth and glycogen content of glgB-deficient and glgB-overexpressing strains showed that the glycogen branching enzyme GlgB is essential for glycogen formation in C. glutamicum. Taken together these results suggest that an interplay of the enzymes GlgC, GlgA and GlgB is not essential for growth, but is required for synthesis of the transient carbon capacitor glycogen in C. glutamicum.
Effect of new alleles of the histidine kinase gene ciaH on the activity of the response regulator CiaR in Streptococcus pneumoniae R6
Authors: Müller Miriam , Marx Patrick , Hakenbeck Regine , Brückner Reinhold
Published: September 2011

The two-component regulatory system CiaRH ofStreptococcus pneumoniaeaffects β-lactam susceptibility, autolysis, bacteriocin production, competence development, host colonization and virulence. The system was discovered in a screen forS. pneumoniaeR6 mutants resistant to the β-lactam antibiotic cefotaxime. A mutation in the histidine kinase geneciaHled to this phenotype by enhancing CiaR-mediated gene expression. Additional mutations inciaHhave been described in other spontaneous β-lactam-resistant mutants ofS.pneumoniaeR6, but their influence on CiaR-mediated gene regulation has not been determined. Likewise, alteredciaHalleles are present in clinicalS. pneumoniaeisolates, none of which had been characterized. These novelciaHvariants were introduced intoS. pneumoniaeR6 to measure their ability to activate CiaR-dependent regulation. TheciaHalleles from spontaneous mutants obtained in the laboratory increased the activity of CiaR-dependent promoters between four- and 26-fold, while variants from clinical strains were less effective, with a threefold activation at most. Accordingly, phenotypes associated with a hyperactive CiaRH system, β-lactam resistance, and prevention of competence development, were far more pronounced in the laboratory mutants. Amino acid changes affecting CiaH function were positioned throughout the protein. Five of the most activating changes are located close to the conserved histidine and one in the extracytoplasmic sensor domain. The characterization of new alleles ofciaHexpands the spectrum of CiaH variants, which may help to elucidate signal transduction of this important regulatory system. Our study also demonstrates thatciaHalleles overstimulating CiaR regulon expression are present in clinical isolates ofS. pneumoniae.
Structural modelling and mutagenesis of human cytomegalovirus alkaline nuclease UL98
Authors: Kuchta Alison L. , Parikh Hardik , Zhu Yali , Kellogg Glen E. , Parris Deborah S. , McVoy Michael A.
Published: September 2011

Human cytomegalovirus encodes an alkaline nuclease, UL98, that is highly conserved among herpesviruses and has both endonuclease (endo) and exonuclease (exo) activities. This protein is thought to be important for viral replication and therefore represents a potential target for antiviral development; however, little is known about its structure or role in viral replication. Comparative structural modelling was used to build a model of UL98 based on the known structure of shutoff and exonuclease protein from Kaposi’s sarcoma-associated herpesvirus. The model predicts that UL98 residues D254, E278 and K280 represent the critical aspartic acid, glutamic acid and lysine active-site residues, respectively, while R164 and S252 correspond to residues proposed to bind the 5′ phosphate of the DNA substrate. UL98 with an amino-terminal hexahistidine tag was expressed inEscherichia coli, purified by affinity chromatography and confirmed to have exo and endo activities. Amino acid substitutions D254A, E278A, K280A and S252A virtually eliminated exo and endo activities, whereas R164A retained full endo activity but only 10 % of the exo activity compared with the wild-type enzyme. A mutant virus lacking UL98 was viable but severely attenuated for replication, while one expressing UL98(R164A) replicated normally. These results confirm the utility of the model in representing the active-site region of UL98 and suggest a mechanism for the differentiation of endonuclease and exonuclease activities. These findings could facilitate the exploration of the roles of alkaline nucleases in herpesvirus replication and the rational design of inhibitors that target their enzymic activities.
Analysis of the human immunodeficiency virus type 1 M group Vpu domains involved in antagonizing tetherin
Authors: Petit Sarah J. , Blondeau Caroline , Towers Greg J.
Published: September 2011

Zoonosis of chimpanzee simian immunodeficiency virus cpz to humans has given rise to both pandemic (M) and non-pandemic (O, N and P) groups of human immunodeficiency virus type-1 (HIV). These lentiviruses encode accessory proteins, including Vpu, which has been shown to reduce CD4 levels on the cell surface, as well as increase virion release from the cell by antagonizing tetherin (CD317, BST2). Here, we confirm that O group Vpus (Ca9 and BCF06) are unable to counteract tetherin or downregulate the protein from the cell surface, although they are still able to reduce cell-surface CD4 levels. We hypothesize that this inability to antagonize tetherin may have contributed to O group viruses failing to achieve pandemic levels of human-to-human transmission. Characterization of chimeric O/M group Vpus and Vpu mutants demonstrate that the Vpu–tetherin interaction is complex, involving several domains. We identify specific residues within the transmembrane proximal region that, along with the transmembrane domain, are crucial for tetherin counteraction and enhanced virion release. We have also shown that the critical domains are responsible for the localization of M group Vpu to thetrans-Golgi network, where it relocalizes tetherin to counteract its function. This work sheds light on the acquisition of anti-tetherin activity and the molecular details of pandemic HIV infection in humans.
Genus-specific recruitment of filovirus ribonucleoprotein complexes into budding particles
Authors: Spiegelberg Larissa , Wahl-Jensen Victoria , Kolesnikova Larissa , Feldmann Heinz , Becker Stephan , Hoenen Thomas
Published: September 2011

The filoviral matrix protein VP40 orchestrates virus morphogenesis and budding. To do this it interacts with both the glycoprotein (GP1,2) and the ribonucleoprotein (RNP) complex components; however, these interactions are still not well understood. Here we show that for efficient VP40-driven formation of transcription and replication-competent virus-like particles (trVLPs), which contain both an RNP complex and GP1,2, the RNP components and VP40, but not GP1,2 and VP40, must be from the same genus. trVLP preparations contained both spherical and filamentous particles, but only the latter were able to infect target cells and to lead to genome replication and transcription. Interestingly, the genus specificity of the VP40–RNP interactions was specific to the formation of filamentous trVLPs, but not to spherical particles. These results not only further our understanding of VP40 interactions, but also suggest that special care is required when using trVLP or VLP systems to model virus morphogenesis.
Walking the tightrope: trends in African freshwater systematic ichthyology
Authors: Skelton P. H. , Swartz E. R.
Published: September 2011

Africa is blessed with an abundance and rich diversity of freshwater fishes, reflecting its Gondwanan history and geographical position astride the equator. Africa is, however, relatively poorly serviced scientifically, in this respect presenting a challenge to the tension between conserving biodiversity and sustainable development. Biosystematics has experienced several paradigm shifts in the past half century, including the rise of cladistics and more recently the adoption of molecular DNA applications to taxonomy and phylogeny and the assembly and manipulation of large data sets in an era of major development of bioinformatics. The richness of African biodiversity is a magnet to the global systematic community that, to a degree, offsets the disadvantage of an impoverished indigenous scientific capacity. Conservation biology, however, is rooted more closely to the local situation and therefore requires indigenous taxonomic services that are inevitably scarce. Balancing this network of tensions between scientific knowledge generation and application is like walking a tightrope for existing African scientific resources, and to cope it is essential to embrace modern innovative approaches such as barcoding to identify organisms. This paper considers the historical development of African freshwater ichthyology, presents a suite of recent examples illustrating trends in systematic ichthyology in Africa and draws conclusions to suggest that both traditional and new‐age approaches to taxonomy are necessary for a complete understanding and appreciation of African freshwater fish diversity and its conservation. The chosen examples also suggest that the tensions between the approaches can be effectively managed provided exponents work collaboratively. The emerging evidence indicates that the combined skills and insight of complex scientific teams including systematists, ecologists, molecular biologists and earth scientists are needed to resolve the deep complexity of evolution in terms of space, time and form.
Molecular phylogeny of the plant bugs (Heteroptera: Miridae) and the evolution of feeding habits
Authors: Jung Sunghoon , Lee Seunghwan
Published: September 2011

The first comprehensive cladistic analysis of Miridae, the plant bugs, is presented based on analysis of 3935 base pairs of mitochondrial (16S, COI) and nuclear (18S, 28SD3) DNA for 91 taxa in seven subfamilies. Data were analysed using maximum likelihood (ML), parsimony and Bayesian inference (BI) phylogenetic frameworks. The phylogenetic results are compared with previous hypotheses of higher relationships in the family using alternative hypothesis tests. A Bayesian relaxed molecular clock is used to examine divergence times, and ancestral feeding habits are reconstructed using parsimony and a Bayesian approach. Clades recovered in all analyses are as follows: Cimicomorpha, Miroidea and Miridae; Bryocorinae: Bryocorini; Stenodemini; Mirinae; Deraeocorinae (Clevinemini + Deraeocorini); Cylapinae; Isometopinae; Bryocorinae: Dicyphini; Orthotylini; Phylinae (Phylini + Pilophorini), and Phylinae as sister group to all the remaining mirid taxa. These results are largely congruent with former hypotheses based on morphological data with respect to the monophyly of various subfamilies and tribes; however, our results indicate that the subfamily Bryocorinae is not monophyletic, as the two tribes, Dicypini and Bryocorini, were separated in the phylogenetic results. Divergence time estimates indicate that the radiation of the Miridae began in the Permian; most genus‐level radiations within subfamilies began in the late Cretaceous, probably in response to the angiosperm radiation. Ancestral feeding state reconstructions based on Bayesian and parsimony inference were largely congruent and both reconstructed phytophagy as the ancestral state of the Miridae. Furthermore, the feeding habits of the common ancestors of Mirinae + Deraeocorinae, Bryocorinae + Cylapinae + Isometopinae + Orthotylinae, and the remaining taxa excluding Phylinae, were inferred as phytophagous. Therefore, at least three shifts from phytophagy or polyphagy to predation occurred within the Miridae. Additionally, based on the mirid host‐plant records, we discovered several trends, such as a strong relationship between host‐plant ranges and a facultative feeding habit.

© The Willi Hennig Society 2011.
Novel epitope evoking CD138 antigen‐specific cytotoxic T lymphocytes targeting multiple myeloma and other plasma cell disorders
Authors: Bae Jooeun , Tai Yu‐Tzu , Anderson Kenneth C. , Munshi Nikhil C.
Published: September 2011

The development of an immunotherapeutic strategy targeting CD138 antigen could potentially represent a new treatment option for multiple myeloma (MM). This study evaluated the immune function of CD138 peptide‐specific cytotoxic T lymphocytes (CTL), generated ex vivo using an HLA‐A2‐specific CD138 epitope against MM cells. A novel immunogenic HLA‐A2‐specific CD138260–268 (GLVGLIFAV) peptide was identified from the full‐length protein sequence of the CD138 antigen, which induced CTL specific to primary CD138+ MM cells. The peptide‐induced CD138‐CTL contained a high percentage of CD8+ activated/memory T cells with a low percentage of CD4+ T cell and naive CD8+ T cell subsets. The CTL displayed HLA‐A2‐restricted and CD138 antigen‐specific cytotoxicity against MM cell lines. In addition, CD138‐CTL demonstrated increased degranulation, proliferation and γ‐interferon secretion to HLA‐A2+/CD138+ myeloma cells, but not HLA‐A2−/CD138+ or HLA‐A2+/CD138− cells. The immune functional properties of the CD138‐CTL were also demonstrated using primary HLA‐A2+/CD138+ cells isolated from myeloma patients. In conclusion, a novel immunogenic CD138260–268 (GLVGLIFAV) peptide can induce antigen‐specific CTL, which might be useful for the treatment of MM patients with peptide‐based vaccine or cellular immunotherapy strategies.
Results of a randomized trial in children with Acute Myeloid Leukaemia: Medical Research Council AML12 trial
Authors: Gibson Brenda E. S. , Webb David K. H. , Howman Andrew J. , De Graaf Siebold S. N. , Harrison Christine J. , Wheatley Keith ,   for the United Kingdom Childhood Leukaemia Working Group and the Dutch Childhood Oncology Group
Published: September 2011

The Medical Research Council Acute Myeloid Leukaemia 12 (MRC AML12) trial (children) addressed the optimal anthracenedione/anthracycline in induction and the optimal number of courses of consolidation chemotherapy. 504 children (<16 years) with AML were randomized between mitoxantrone/cytarabine/etoposide or daunorubicin/cytarabine/etoposide as induction chemotherapy and 270 entered a second randomization between a total of four or five courses of treatment. Ten‐year event‐free (EFS) and overall survival (OS) was 54% and 63% respectively; the relapse rate was 35%. There was no difference in complete remission rate between the induction regimens, but there was a benefit for mitoxantrone with regard to relapse rate [32% vs. 39%; Hazard ratio (HR) 0·73; 95% confidence interval (CI) 0·54, 1·00] and disease‐free survival (DFS; 63% vs. 55%; HR 0·72; 95% CI 0·54, 0·96). However, this did not translate into a better EFS or OS (HR 0·84; 95% CI 0·63, 1·12). Results of the second randomization did not show a survival benefit for a fifth course of treatment (HR 1·01; 95% CI 0·63, 1·62), suggesting a ceiling of benefit for conventional chemotherapy and demonstrating the need for new agents. EFS was superior compared to the preceding trial AML10, partly due to fewer deaths in remission, highlighting the importance of supportive care.
Could exhaled ferritin and SOD be used as markers for lung cancer and prognosis prediction purposes?
Authors: Carpagnano Giovanna E. , Lacedonia Donato , Palladino Grazia P. , Koutelou Anna , Martinelli Domenico , Orlando Silvio , Foschino‐Barbaro Maria P.
Published: September 2011

Eur J Clin Invest 2012; 42 (5): 478–486

Background  Today an increasing interest is being generated by the study of lung cancer markers in the exhaled breath condensate (EBC), precisely because this sample seems to lend itself to lung cancer early screening and follow‐up. Indeed, ferritin and superoxide dismutase (SOD) have recently been recognized to play a role in lung cancerogenesis and patients’ survival. The aim of this study was to evaluate the clinical value and the prognostic power of exhaled ferritin and exhaled SOD in patients with lung cancer.

Material and methods  Forty patients with nonsmall cell lung cancer (NSCLC) and 15 controls were enrolled in the study. All subjects under study underwent EBC collection and analysis of ferritin and SOD. A total of 36 patients were either given a follow‐up of at least 25·5 months or followed up until death.

Results  Exhaled ferritin and SOD resulted as being higher in NSCLC than in controls and as being influenced by the stage of cancer. A pronounced survival difference was found in the presence of exhaled ferritin 300 ng/mL and exhaled SOD > 13·5 U/μL.

Conclusions  In conclusion, although the results need to be confirmed on a larger and homogeneous population, we hypothesized that the notion of using the measurement of ferritin and SOD in the EBC could, if deemed feasible, have clinical implications in the monitoring of lung cancer and as an outcome predictor.
Outcomes of mentored, grant‐funded fellowship training in haemostasis /thrombosis: findings from a nested case–control survey study
Authors: GOLDENBERG N. A. , KRUSE‐JARRES R. , FRICK N. , PIPE S. W. , LEISSINGER C. A. , KESSLER C. M.
Published: September 2011

Summary.  Successful strategies by which to effectively recruit and retain academic subspecialists in benign haematology have not been established. To evaluate the effectiveness of a grant‐funded, mentored fellowship with respect to retention and early career goals in haemostasis/thrombosis, we sought to compare outcomes for graduates of a grant‐funded, mentored fellowship training programme in haemostasis/thrombosis [the National Hemophilia Foundation (NHF)‐Baxter Clinical Fellowship Award] during conventional haematology/oncology fellowship training (cases), vs. their training peers who were graduates of conventional haematology/oncology fellowship training alone (controls), via a nested case‐control survey study. Survey response rate was 85% (11/13) for cases and 90% (9/10) for controls. All respondents had pursued careers in academic haematology/oncology. Median (range) percent time spent in benign haematology postfellowship was 98% (70–100%) for cases vs. 0% (0–20%) for controls. Time spent in research was significantly greater among cases than controls (median 80% [range: 42–90%] vs. 55% [10–80%], respectively; P = 0.01). By years 3–4 postfellowship, median annual number of peer‐reviewed publications was higher for cases than controls (3.5 vs. 1.0; P = 0.01). Cases were also more successful in grant funding (including K‐awards). These data suggest that a grant‐funded, mentored fellowship training programme in haemostasis/thrombosis may be superior to conventional haematology/oncology fellowship training alone with respect to outcomes of retention in clinical care/research, early‐career grant funding and publication productivity.