bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatiotemporal regulation of chemical reactions by active cytoskeletal remodeling
Authors: Chaudhuri Abhishek , Bhattacharya Bhaswati , Gowrishankar Kripa , Mayor Satyajit , Rao Madan
Published: August 2011

Efficient and reproducible construction of signaling and sorting complexes, both on the surface and within the living cell, is contingent on local regulation of biochemical reactions by the cellular milieu. We propose that in many cases this spatiotemporal regulation can be mediated by interaction with components of the dynamic cytoskeleton. We show how the interplay between active contractility and remodeling of the cytoskeleton can result in transient focusing of passive molecules to form clusters, leading to a dramatic increase in the reaction efficiency and output levels. The dynamic cytoskeletal elements that drive focusing behave asquasienzymescatalyzing the chemical reaction. These ideas are directly applicable to the cortical actin-dependent clustering of cell surface proteins such as lipid-tethered GPI-anchored proteins, Ras proteins, as well as many proteins that have domains that confer the ability to interact with the actin cytoskeleton. In general such cytoskeletal driven clustering of proteins could be a cellular mechanism to spatiotemporally regulate and amplify local chemical reaction rates in a variety of contexts such as signaling, transcription, sorting, and endocytosis.
Tsukushi functions as a Wnt signaling inhibitor by competing with Wnt2b for binding to transmembrane protein Frizzled4
Authors: Ohta Kunimasa , Ito Ayako , Kuriyama Sei , Lupo Giuseppe , Kosaka Mitsuko , Ohnuma Shin-ichi , Nakagawa Shinichi , Tanaka Hideaki
Published: August 2011

The Wnt signaling pathway is essential for the development of diverse tissues during embryogenesis. Signal transduction is activated by the binding of Wnt proteins to the type I receptor low-density lipoprotein receptor–related protein 5/6 and the seven-pass transmembrane protein Frizzled (Fzd), which contains a Wnt-binding site in the form of a cysteine-rich domain. Known extracellular antagonists of the Wnt signaling pathway can be subdivided into two broad classes depending on whether they bind primarily to Wnt or to low-density lipoprotein receptor–related protein 5/6. We show that the secreted protein Tsukushi (TSK) functions as a Wnt signaling inhibitor by binding directly to the cysteine-rich domain of Fzd4 with an affinity of 2.3 × 10−10M and competing with Wnt2b. In the developing chick eye, TSK is expressed in the ciliary/iris epithelium, whereas Wnt2b is expressed in the adjacent anterior rim of the optic vesicle, where it controls the differentiation of peripheral eye structures, such as the ciliary body and iris. TSK overexpression effectively antagonizes Wnt2b signaling in chicken embryonic retinal cells both in vivo and in vitro and represses Wnt-dependent specification of peripheral eye fates. Conversely, targeted inactivation of the TSK gene in mice causes expansion of the ciliary body and up-regulation of Wnt2b and Fzd4 expression in the developing peripheral eye. Thus, we uncover a crucial role for TSK as a Wnt signaling inhibitor that regulates peripheral eye formation.
The RND-family transporter, HpnN, is required for hopanoid localization to the outer membrane of
Rhodopseudomonas palustris
TIE-1
Authors: Doughty David M. , Coleman Maureen L. , Hunter Ryan C. , Sessions Alex L. , Summons Roger E. , Newman Dianne K.
Published: August 2011

Rhodopseudomonas palustris
TIE-1 is a Gram-negative bacterium that produces structurally diverse hopanoid lipids that are similar to eukaryotic steroids. Its genome encodes several homologues to proteins involved in eukaryotic steroid trafficking. In this study, we explored the possibility that two of these proteins are involved in intracellular hopanoid transport.
R. palustris
has a sophisticated membrane system comprising outer, cytoplasmic, and inner cytoplasmic membranes. It also divides asymmetrically, producing a mother and swarmer cell. We deleted genes encoding two putative hopanoid transporters that belong to the resistance–nodulation–cell division superfamily. Phenotypic analyses revealed that one of these putative transporters (HpnN) is essential for the movement of hopanoids from the cytoplasmic to the outer membrane, whereas the other (Rpal_4267) plays a minor role. C
30
hopanoids, such as diploptene, are evenly distributed between mother and swarmer cells, whereas
hpnN
is required for the C
35
hopanoid, bacteriohopanetetrol, to remain localized to the mother cell type. Mutant cells lacking HpnN grow like the WT at 30 °C but slower at 38 °C. Following cell division at 38 °C, the
ΔhpnN
cells remain connected by their cell wall, forming long filaments. This phenotype may be attributed to hopanoid mislocalization because a double mutant deficient in both hopanoid biosynthesis and transport does not form filaments. However, the lack of hopanoids severely compromises cell growth at higher temperatures more generally. Because hopanoid mutants only manifest a strong phenotype under certain conditions,
R. palustris
is an attractive model organism in which to study their transport and function.
Stability of plant immune-receptor resistance proteins is controlled by SKP1-CULLIN1-F-box (SCF)-mediated protein degradation
Authors: Cheng Yu Ti , Li Yingzhong , Huang Shuai , Huang Yan , Dong Xinnian , Zhang Yuelin , Li Xin
Published: August 2011

The nucleotide-binding domain and leucine-rich repeats containing proteins (NLRs) serve as immune receptors in both plants and animals. Overaccumulation of NLRs often leads to autoimmune responses, suggesting that the levels of these immune receptors must be tightly controlled. However, the mechanism by which NLR protein levels are regulated is unknown. Here we report that the F-box protein CPR1 controls the stability of plant NLR resistance proteins. Loss-of-function mutations in
CPR1
lead to higher accumulation of the NLR proteins SNC1 and RPS2, as well as autoactivation of immune responses. The autoimmune responses in
cpr1
mutant plants can be largely suppressed by knocking out
SNC1
. Furthermore, CPR1 interacts with SNC1 and RPS2 in vivo, and overexpressing
CPR1
results in reduced accumulation of SNC1 and RPS2, as well as suppression of immunity mediated by these two NLR proteins. Our data suggest that SKP1-CULLIN1-F-box (SCF) complex-mediated stability control of plant NLR proteins plays an important role in regulating their protein levels and preventing autoimmunity.
Tracking a defined route for O
2
migration in a dioxygen-activating diiron enzyme
Authors: Song Woon Ju , Gucinski Grant , Sazinsky Matthew H. , Lippard Stephen J.
Published: August 2011

For numerous enzymes reactive toward small gaseous compounds, growing evidence indicates that these substrates diffuse into active site pockets through defined pathways in the protein matrix. Toluene/
o
-xylene monooxygenase hydroxylase is a dioxygen-activating enzyme. Structural analysis suggests two possible pathways for dioxygen access through the α-subunit to the diiron center: a channel or a series of hydrophobic cavities. To distinguish which is utilized as the O
2
migration pathway, the dimensions of the cavities and the channel were independently varied by site-directed mutagenesis and confirmed by X-ray crystallography. The rate constants for dioxygen access to the diiron center were derived from the formation rates of a peroxodiiron(III) intermediate, generated upon treatment of the diiron(II) enzyme with O
2
. This reaction depends on the concentration of dioxygen to the first order. Altering the dimensions of the cavities, but not the channel, changed the rate of dioxygen reactivity with the enzyme. These results strongly suggest that voids comprising the cavities in toluene/
o
-xylene monooxygenase hydroxylase are not artifacts of protein packing/folding, but rather programmed routes for dioxygen migration through the protein matrix. Because the cavities are not fully connected into the diiron active center in the enzyme resting state, conformational changes will be required to facilitate dioxygen access to the diiron center. We propose that such temporary opening and closing of the cavities may occur in all bacterial multicomponent monooxygenases to control O
2
consumption for efficient catalysis. Our findings suggest that other gas-utilizing enzymes may employ similar structural features to effect substrate passage through a protein matrix.
Human Polymerase-Associated Factor complex (PAFc) connects the Super Elongation Complex (SEC) to RNA polymerase II on chromatin
Authors: He Nanhai , Chan Caleb K. , Sobhian Bijan , Chou Seemay , Xue Yuhua , Liu Min , Alber Tom , Benkirane Monsef , Zhou Qiang
Published: August 2011

The Super Elongation Complex (SEC), containing transcription elongation activators/coactivators P-TEFb, ELL2, AFF4/1, ENL, and AF9, is recruited by HIV-1 Tat and mixed lineage leukemia (MLL) proteins to activate the expression of HIV-1 and MLL-target genes, respectively. In the absence of Tat and MLL, however, it is unclear how SEC is targeted to RNA polymerase (Pol) II to stimulate elongation in general. Furthermore, although ENL and AF9 can bind the H3K79 methyltransferase Dot1L, it is unclear whether these bindings are required for SEC-mediated transcription. Here, we show that the homologous ENL and AF9 exist in separate SECs with similar but nonidentical functions. ENL/AF9 contacts the scaffolding protein AFF4 that uses separate domains to recruit different subunits into SEC. ENL/AF9 also exists outside SEC when bound to Dot1L, which is found to inhibit SEC function. The YEATS domain of ENL/AF9 targets SEC to Pol II on chromatin through contacting the human Polymerase-Associated Factor complex (PAFc) complex. This finding explains the YEATS domain’s dispensability for leukemogenesis when ENL/AF9 is translocated to MLL, whose interactions with PAFc and DNA likely substitute for the PAFc/chromatin-targeting function of the YEATS domain.
Protons migrate along interfacial water without significant contributions from jumps between ionizable groups on the membrane surface
Authors: Springer Andreas , Hagen Volker , Cherepanov Dmitry A. , Antonenko Yuri N. , Pohl Peter
Published: August 2011

Proton diffusion along membrane surfaces is thought to be essential for many cellular processes such as energy transduction. Commonly, it is treated as a succession of jumps between membrane-anchored proton-binding sites. Our experiments provide evidence for an alternative model. We released membrane-bound caged protons by UV flashes and monitored their arrival at distant sites by fluorescence measurements. The kinetics of the arrival is probed as a function of distance for different membranes and for different water isotopes. We found that proton diffusion along the membrane is fast even in the absence of ionizable groups in the membrane, and it decreases strongly in D
2
O as compared to H
2
O. We conclude that the fast proton transport along the membrane is dominated by diffusion via interfacial water, and not via ionizable lipid moieties.
Three-dimensional structure and function of the
Paramecium bursaria
chlorella virus capsid
Authors: Zhang Xinzheng , Xiang Ye , Dunigan David D. , Klose Thomas , Chipman Paul R. , Van Etten James L. , Rossmann Michael G.
Published: August 2011

A cryoelectron microscopy 8.5 Å resolution map of the 1,900 Å diameter, icosahedral, internally enveloped
Paramecium bursaria
chlorella virus was used to interpret structures of the virus at initial stages of cell infection. A fivefold averaged map demonstrated that two minor capsid proteins involved in stabilizing the capsid are missing in the vicinity of the unique vertex. Reconstruction of the virus in the presence of host chlorella cell walls established that the spike at the unique vertex initiates binding to the cell wall, which results in the enveloped nucleocapsid moving closer to the cell. This process is concurrent with the release of the internal viral membrane that was linked to the capsid by many copies of a viral membrane protein in the mature infectous virus. Simultaneously, part of the trisymmetrons around the unique vertex disassemble, probably in part because two minor capsid proteins are absent, causing
Paramecium bursaria
chlorella virus and the cellular contents to merge, possibly as a result of enzyme(s) within the spike assembly. This may be one of only a few recordings of successive stages of a virus while infecting a eukaryotic host in pseudoatomic detail in three dimensions.
Age-related changes in the plasticity and toughness of human cortical bone at multiple length scales
Authors: Zimmermann Elizabeth A. , Schaible Eric , Bale Hrishikesh , Barth Holly D. , Tang Simon Y. , Reichert Peter , Busse Bjoern , Alliston Tamara , Ager Joel W. , Ritchie Robert O.
Published: August 2011

The structure of human cortical bone evolves over multiple length scales from its basic constituents of collagen and hydroxyapatite at the nanoscale to osteonal structures at near-millimeter dimensions, which all provide the basis for its mechanical properties. To resist fracture, bone’s toughness is derived intrinsically through plasticity (e.g., fibrillar sliding) at structural scales typically below a micrometer and extrinsically (i.e., during crack growth) through mechanisms (e.g., crack deflection/bridging) generated at larger structural scales. Biological factors such as aging lead to a markedly increased fracture risk, which is often associated with an age-related loss in bone mass (bone quantity). However, we find that age-related structural changes can significantly degrade the fracture resistance (bone quality) over multiple length scales. Using in situ small-angle X-ray scattering and wide-angle X-ray diffraction to characterize submicrometer structural changes and synchrotron X-ray computed tomography and in situ fracture-toughness measurements in the scanning electron microscope to characterize effects at micrometer scales, we show how these age-related structural changes at differing size scales degrade both the intrinsic and extrinsic toughness of bone. Specifically, we attribute the loss in toughness to increased nonenzymatic collagen cross-linking, which suppresses plasticity at nanoscale dimensions, and to an increased osteonal density, which limits the potency of crack-bridging mechanisms at micrometer scales. The link between these processes is that the increased stiffness of the cross-linked collagen requires energy to be absorbed by “plastic” deformation at higher structural levels, which occurs by the process of microcracking.
Sirtuin-3 (Sirt3) regulates skeletal muscle metabolism and insulin signaling via altered mitochondrial oxidation and reactive oxygen species production
Authors: Jing Enxuan , Emanuelli Brice , Hirschey Matthew D. , Boucher Jeremie , Lee Kevin Y. , Lombard David , Verdin Eric M. , Kahn C. Ronald
Published: August 2011

Sirt3
is a member of the sirtuin family of protein deacetylases that is localized in mitochondria and regulates mitochondrial function.
Sirt3
expression in skeletal muscle is decreased in models of type 1 and type 2 diabetes and regulated by feeding, fasting, and caloric restriction.
Sirt3
knockout mice exhibit decreased oxygen consumption and develop oxidative stress in skeletal muscle, leading to JNK activation and impaired insulin signaling. This effect is mimicked by knockdown of
Sirt3
in cultured myoblasts, which exhibit reduced mitochondrial oxidation, increased reactive oxygen species, activation of JNK, increased serine and decreased tyrosine phosphorylation of IRS-1, and decreased insulin signaling. Thus,
Sirt3
plays an important role in diabetes through regulation of mitochondrial oxidation, reactive oxygen species production, and insulin resistance in skeletal muscle.
Mobilization of natural killer cells inhibits development of collagen-induced arthritis
Authors: Leavenworth Jianmei W. , Wang Xiaoyang , Wenander Carola Schellack , Spee Pieter , Cantor Harvey
Published: August 2011

Although natural killer (NK) cells have been implicated in regulating immune responses, their ability to modulate disease development in autoimmune arthritis has not been analyzed. Here we investigate the contribution of NK cells to regulating collagen-induced arthritis, a well-characterized preclinical model of human rheumatoid arthritis. We find that the disease is induced by the combined action of two CD4
+
T helper (T
H
) subsets: follicular T
H
cells and T
H
17 cells. Both CD4
+
T
H
subsets are highly susceptible to lysis by NK cells after activation. Administration of antibody that activates NK cells through blockade of its inhibitory CD94/NKG2A receptor allows enhanced elimination of pathogenic follicular T
H
and T
H
17 cells and arrest of disease progression. These results suggest that antibody-dependent enhancement of NK activity may yield effective, previously undescribed therapeutic approaches to this autoimmune disorder.
Individual differences in child English second language acquisition
Authors: Paradis Johanne
Published: August 2011

This study investigated how various child-internal and child-external factors predict English L2 children’s acquisition outcomes for vocabulary size and accuracy with verb morphology. The children who participated (N=169) were between 4;10 and 7;0 years old (mean = 5;10), had between 3 to 62 months of exposure to English (mean = 20 months), and were from newcomer families to Canada. Results showed that factors such as language aptitude (phonological short term memory and analytic reasoning), age, L1 typology, length of exposure to English, and richness of the child’s English environment were significant predictors of variation in children’s L2 outcomes. However, on balance, child-internal factors explained more of the variance in outcomes than child-external factors. Relevance of these findings for Usage-Based theory of language acquisition is discussed.
Recognizing sarcasm without language
Authors: Cheang Henry S. , Pell Marc D.
Published: August 2011

The goal of the present research was to determine whether certain speaker intentions conveyed through prosody in an unfamiliar language can be accurately recognized. English and Cantonese utterances expressing sarcasm, sincerity, humorous irony, or neutrality through prosody were presented to English and Cantonese listeners unfamiliar with the other language. Listeners identified the communicative intent of utterances in both languages in a crossed design. Participants successfully identified sarcasm spoken in their native language but identified sarcasm at near-chance levels in the unfamiliar language. Both groups were relatively more successful at recognizing the other attitudes when listening to the unfamiliar language (in addition to the native language). Our data suggest that while sarcastic utterances in Cantonese and English share certain acoustic features, these cues are insufficient to recognize sarcasm between languages; rather, this ability depends on (native) language experience.
Targeting cap-dependent translation blocks converging survival signals by AKT and PIM kinases in lymphoma
Authors: Schatz Jonathan H. , Oricchio Elisa , Wolfe Andrew L. , Jiang Man , Linkov Irina , Maragulia Jocelyn , Shi Weiji , Zhang Zhigang , Rajasekhar Vinagolu K. , Pagano Nen C. , Porco John A. , Teruya-Feldstein Julie , Rosen Neal , Zelenetz Andrew D. , Pelletier Jerry , Wendel Hans-Guido
Published: August 2011

New anticancer drugs that target oncogenic signaling molecules have greatly improved the treatment of certain cancers. However, resistance to targeted therapeutics is a major clinical problem and the redundancy of oncogenic signaling pathways provides back-up mechanisms that allow cancer cells to escape. For example, the AKT and PIM kinases produce parallel oncogenic signals and share many molecular targets, including activators of cap-dependent translation. Here, we show that PIM kinase expression can affect the clinical outcome of lymphoma chemotherapy. We observe the same in animal lymphoma models. Whereas chemoresistance caused by AKT is readily reversed with rapamycin, PIM-mediated resistance is refractory to mTORC1 inhibition. However, both PIM- and AKT-expressing lymphomas depend on cap-dependent translation, and genetic or pharmacological blockade of the translation initiation complex is highly effective against these tumors. The therapeutic effect of blocking cap-dependent translation is mediated, at least in part, by decreased production of short-lived oncoproteins including c-MYC, Cyclin D1, MCL1, and the PIM1/2 kinases themselves. Hence, targeting the convergence of oncogenic survival signals on translation initiation is an effective alternative to combinations of kinase inhibitors.
Investigating the flow dynamics and chemistry of an expanding thermal plasma through CH(A–X) emission spectra
Authors: Hansen T A R , Colsters P G J , van de Sanden M C M , Engeln R
Published: August 2011

The gas flow in a linear plasma reactor and the plasma chemistry during hydrogenated amorphous carbon and graphite etching are investigated via time and spatially resolved measurements of the ion density and CH emission. A convolution of the ion and hydrocarbon density shows the importance of charge transfer in the plasma chemistry which ultimately yields the CH emission. The spatially resolved measurements clearly visualize the plasma expansion in the reactor and its deflection on a substrate. A stagnation zone is furthermore formed in front of a substrate when placed inside an expanding thermal plasma. An increased ion density further upstream from the substrate is attributed to a reorganization of the gas recirculation cells in the background of the reactor. The movement of a shutter in and out of the plasma expansion likewise affects these recirculation cells. This movement consequently redirects the energy flow to and from the background, as is deduced from the variation in rotational temperature of the CH radical.
Lithium–metal infused trenches (LiMIT) for heat removal in fusion devices
Authors: Ruzic D.N. , Xu W. , Andruczyk D. , Jaworski M.A.
Published: August 2011

Observation of liquid lithium flow in metal trenches has been made using a lithium–metal infused trench (LiMIT) tile and is reported here. The flow is self-pumping and uses thermoelectric magnetohydrodynamics to remove heated lithium and replenish it at a lower temperature. Flow velocities have been measured and compared with theoretical predictions.
Requirements on localized current drive for the suppression of neoclassical tearing modes
Authors: Bertelli N. , De Lazzari D. , Westerhof E.
Published: August 2011

A heuristic criterion for the full suppression of an NTM was formulated as ηNTM ≡ j
CD,max/j
BS ⩾ 1.2 (Zohm et al 2005 J. Phys. Conf. Ser.
25 234), where j
CD,max is the maximum in the driven current density profile applied to stabilize the mode and j
BS is the local bootstrap current density. In this work we subject this criterion to a systematic theoretical analysis on the basis of the generalized Rutherford equation. Taking into account only the effect of j
CD inside the island, a new criterion for full suppression by a minimum applied total current is obtained in the form of a maximum allowed value for the width of the driven current, w
dep, combined with a required minimum for the total driven current in the form of w
depηNTM, where both limits depend on the marginal and saturated island sizes. These requirements can be relaxed when additional effects are taken into account, such as a change in the stability parameter Δ′ from the current driven outside the island, power modulation, the accompanying heating inside the island or when the current drive is applied preemptively. When applied to ITER scenario 2, the requirement for full suppression of either the 3/2 or 2/1 NTM becomes w
dep ≲ 5 cm and w
depηNTM ≳ 5 cm in agreement with (Sauter et al
2010 Plasma Phys. Control. Fusion
52 025002). Optimization of the ITER ECRH Upper Port Launcher design towards minimum required power for full NTM suppression requires an increase in the toroidal injection angle of the lower steering mirror of several degrees compared with its present design value, while for the upper steering mirror the present design value is close to the optimum.
An ICF system based on Z-pinch radiation produced by an explosive magnetic generator
Authors: Garanin S.G. , Ivanovsky A.V. , Mkhitariyan L.S.
Published: August 2011

It is known that a thermonuclear target can be ignited by an implosion accomplished with X-radiation generated by means of laser radiation conversion or by a Z pinch formed by a high-power current pulse. For these purposes laser facility NIF has been constructed in the USA, ‘Megajoule’ is being constructed in France and there is a project of laser facility UFL in Russia. The project of stationary facility X has been developed in SNL USA to produce a Z pinch capable of generating an x-ray pulse with parameters close to the ignition threshold. There is a great chance, however, that the already tested technologies, including disc explosive magnetic generators (DEMG), systems of current peaking based on electrically exploded foil opening switches and high-voltage switching devices, allow the intriguing problem of the ignition feasibility to be solved and the quickest and cheapest way to accomplish this to be provided. To explore this possibility, the paper will sequentially analyse the ignition conditions. The required parameters of Z pinch X-radiation and the size of the DEMG-based facility to obtain these parameters will be evaluated. Capabilities of the new current sources based on the DEMG and of the devices shaping a current pulse will be presented and compared with those required for the ignition.
Study on fission blanket fuel cycling of a fusion–fission hybrid energy generation system
Authors: Zhou Z. , Yang Y. , Xu H.
Published: August 2011

This paper presents a preliminary study on neutron physics characteristics of a light water cooled fission blanket for a new type subcritical fusion–fission hybrid reactor aiming at electric power generation with low technical limits of fission fuel. The major objective is to study the fission fuel cycling performance in the blanket, which may possess significant impacts on the feasibility of the new concept of fusion–fission hybrid reactor with a high energy gain (M) and tritium breeding ratio (TBR). The COUPLE2 code developed by the Institute of Nuclear and New Energy Technology of Tsinghua University is employed to simulate the neutronic behaviour in the blanket. COUPLE2 combines the particle transport code MCNPX with the fuel depletion code ORIGEN2. The code calculation results show that soft neutron spectrum can yield M > 20 while maintaining TBR >1.15 and the conversion ratio of fissile materials CR > 1 in a reasonably long refuelling cycle (>five years). The preliminary results also indicate that it is rather promising to design a high-performance light water cooled fission blanket of fusion–fission hybrid reactor for electric power generation by directly loading natural or depleted uranium if an ITER-scale tokamak fusion neutron source is achievable.
Fast-ion transport induced by Alfvén eigenmodes in the ASDEX Upgrade tokamak
Authors: Garcia-Munoz M. , Classen I.G.J. , Geiger B. , Heidbrink W.W. , Van Zeeland M.A. , Äkäslompolo S. , Bilato R. , Bobkov V. , Brambilla M. , Conway G.D. , Graça S. da , Igochine V. , Lauber Ph. , Luhmann N. , Maraschek M. , Meo F. , Park H. , Schneller M. , Tardini G.
Published: August 2011

A comprehensive suite of diagnostics has allowed detailed measurements of the Alfvén eigenmode (AE) spatial structure and subsequent fast-ion transport in the ASDEX Upgrade (AUG) tokamak [1]. Reversed shear Alfvén eigenmodes (RSAEs) and toroidal induced Alfvén eigenmodes (TAEs) have been driven unstable by fast ions from ICRH as well as NBI origin. In ICRF heated plasmas, diffusive and convective fast-ion losses induced by AEs have been characterized in fast-ion phase space. While single RSAEs and TAEs eject resonant fast ions in a convective process directly proportional to the fluctuation amplitude, δB/B, the overlapping of multiple RSAE and TAE spatial structures and wave–particle resonances leads to a large diffusive loss, scaling as (δB/B)2. In beam heated discharges, coherent fast-ion losses have been observed primarily due to TAEs. Core localized, low amplitude NBI driven RSAEs have not been observed to cause significant coherent fast-ion losses. The temporal evolution of the confined fast-ion profile in the presence of RSAEs and TAEs has been monitored with high spatial and temporal resolution. A large drop in the central fast-ion density due to many RSAEs has been observed as q
min passes through an integer. The AE radial and poloidal structures have been obtained with unprecedented details using a fast SXR as well as 1D and 2D ECE radiometers. GOURDON and HAGIS simulations have been performed to identify the orbit topology of the escaping ions and study the transport mechanisms. Both passing and trapped ions are strongly redistributed by AEs.
Analytic expressions for shaping analysis of the ITER outer wall
Authors: Stangeby Peter
Published: August 2011

Divertor tokamaks such as ITER also need limiters for startup and rampdown, as well as protection of the main wall from normal and off-normal plasma loads during the diverted phase. Analysis of the optimum shape with regard to power handling of the plasma-facing surface is typically carried out using numerical procedures. This can make it difficult to identify underlying shaping principles. It is also important to have methods for conveniently and quickly checking the correctness of numerical results, approximately, using readily available analytic expressions. This paper provides such expressions together with their derivations for the case of multiple limiters at the outer wall, low-field side of a tokamak, illustrated here for the case of ITER. Analytic expressions are developed for the near-optimal toroidal shaping of individual limiters which, while distributing the deposited power on the limiter face as uniformly as possible, also provides adequate protection of the limiter edges against over-heating—for a range of plasma shapes and conditions and for a specified number of limiters, limiter sizes, sizes of gaps between limiters and relative radial misalignment between adjacent limiters. The effect of shadowing of one limiter by another is included, for shadowing of both edges and faces. Analytic expressions are developed for the magnitude and location of the peak power flux density deposited on the face and edges of the limiters. There are sufficient important differences in the shaping required for wall regions on the low- and high-field sides and in the secondary divertor region at the top of the vessel to warrant separate treatments of each of the three cases. In subsequent papers analytic expressions will be developed for the inner wall and the top wall.
A first-principles predictive model of the pedestal height and width: development, testing and ITER optimization with the EPED model
Authors: Snyder P.B. , Groebner R.J. , Hughes J.W. , Osborne T.H. , Beurskens M. , Leonard A.W. , Wilson H.R. , Xu X.Q.
Published: August 2011

We develop and test a model, EPED1.6, for the H-mode pedestal height and width based upon two fundamental and calculable constraints: (1) onset of non-local peeling–ballooning modes at low to intermediate mode number, (2) onset of nearly local kinetic ballooning modes at high mode number. Calculation of these two constraints allows a unique, predictive determination of both pedestal height and width. The present version of the model is first principles, in that no parameters are fit to observations, and includes important non-ideal effects. Extensive successful comparisons with existing experiments on multiple tokamaks, including experiments where predictions were made prior to the experiment, are presented, and predictions for ITER are discussed.
PTPan—overcoming memory limitations in oligonucleotide string matching for primer/probe design
Authors: Eißler Tilo , Hodges Christopher P. , Meier Harald
Published: August 2011

Motivation: Nucleic acid diagnostics has high demands for non-heuristic exact and approximate oligonucleotide string matching concerning in silico primer/probe design in huge nucleic acid sequence collections. Unfortunately, public sequence repositories grow much faster than computer hardware performance and main memory capacity do. This growth imposes severe problems on existing oligonucleotide primer/probe design applications necessitating new approaches based on space-efficient indexing structures.

Results: We developed PTPan (spoken Peter Pan, ‘PT’ is for Position Tree, the earlier name of suffix trees), a space-efficient indexing structure for approximate oligonucleotide string matching in nucleic acid sequence data. Based on suffix trees, it combines partitioning, truncation and a new suffix tree stream compression to deal with large amounts of aligned and unaligned data. PTPan operates efficiently in main memory and on secondary storage, balancing between memory consumption and runtime during construction and application. Based on PTPan, applications supporting similarity search and primer/probe design have been implemented, namely FindFamily, ProbeMatch and ProbeDesign. All three use a weighted Levenshtein distance metric for approximative queries to find and rate matches with indels as well as substitutions.

We integrated PTPan in the worldwide used software package ARB to demonstrate usability and performance. Comparing PTPan and the original ARB index for the very large ssu-rRNA database SILVA, we recognized a shorter construction time, extended functionality and dramatically reduced memory requirements at the price of expanded, but very reasonable query times.

PTPan enables indexing of huge nucleic acid sequence collections at reasonable application response times. Not being limited by main memory, PTPan constitutes a major advancement regarding rapid oligonucleotide string matching in primer/probe design now and in the future facing the enormous growth of molecular sequence data.

Availability:  Supplementary Material, PTPan stand-alone library and ARB-PTPan binary on http://ptpan.lrr.in.tum.de/.

Contact:  meierh@in.tum.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Leuconostoc mesenteroides subsp. suionicum subsp. nov.
Authors: Gu Chun Tao , Wang Fang , Li Chun Yan , Liu Fei , Huo Gui Cheng
Published: August 2011

Strains LMG 8159 and LMG 11499 were reclassified by a polyphasic approach, including 16S rRNA gene sequence analysis, 16S–23S rRNA intergenic spacer (IGS) sequence analysis, (GTG)5-PCR fingerprinting, RAPD fingerprinting, fatty acid methyl ester analysis and an analysis of phenotypic features using API 50 CH. The two strains were closely related to the type strains of the three defined subspecies of

Leuconostoc mesenteroides

, showing 99.7–99.9 % 16S rRNA gene sequence similarity, 99.2 % 16S–23S rRNA gene intergenic spacer sequence similarity, 97.1–97.4 % pheS gene sequence similarity and 98.0–98.2 % rpoA gene sequence similarity. Low atpA gene sequence similarity (91.4–91.7 %), (GTG)5-PCR fingerprinting, RAPD fingerprinting, fatty acid compositions and phenotypic features allowed us to differentiate strains LMG 8159 and LMG 11499 from all established subspecies within

L. mesenteroides

. Based upon the data obtained in the present and previous studies, a novel subspecies is proposed within the species

L. mesenteroides

, Leuconostoc mesenteroides subsp. suionicum subsp. nov., with the type strain LMG 8159T ( = ATCC 9135T  = DSM 20241T  = NCIMB 6992T).
Oceanisphaera

sediminis sp. nov., isolated from marine sediment
Authors: Shin Na-Ri , Whon Tae Woong , Roh Seong Woon , Kim Min-Soo , Kim Young-Ok , Bae Jin-Woo
Published: August 2011

Two strains, designated TW92T and TW93, were isolated from marine sediment collected from the south coast of Korea. Cells of both strains were Gram-staining-negative, coccus-shaped, aerobic, motile and catalase- and oxidase-positive. Strain TW92T grew optimally in the presence of 2 % (w/v) NaCl (range 1–5 %) while strain TW93 grew optimally in the presence of 1 % (w/v) NaCl (range 0–12 %), and both strains had an optimal growth temperature of 30 °C (range 4–37 °C). Strains TW92T and TW93 had the same optimum pH (pH 7), but differed in their ability to grow at pH 10. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strains TW92T and TW93 were most closely related to

Oceanisphaera donghaensis

BL1T, with 98.8 % and 98.7 % similarity, respectively. Pairwise similarity between the 16S rRNA gene sequences of strains TW92T and TW93 was 99.9 %. The major fatty acids of both strains were summed features 3 (comprising C16 : 1ω7c/iso-C15 2-OH), C16 : 0 and C18 : 1ω7c. Both strains possessed the ubiquinone Q-8 as the predominant respiratory quinone and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as the polar lipids. The genomic DNA G+C contents of strains TW92T and TW93 were 58.5 and 59.6 mol%, respectively. Genomic relatedness values based on DNA–DNA hybridization of strains TW92T and TW93 with related species were below 47 % and 31 %, respectively. DNA–DNA hybridization values between strains TW92T and TW93 were above 85 %. On the basis of a taxonomic study using polyphasic analysis, it is proposed that the two isolates represent a novel species,
Oceanisphaera

sediminis sp. nov., with strain TW92T ( = KACC 15117T = JCM 17329T) as the type strain and strain TW93 ( = KACC 15118 = JCM 17330) as an additional strain.
Acidicapsa borealis gen. nov., sp. nov. and Acidicapsa ligni sp. nov., subdivision 1

Acidobacteria

from Sphagnum peat and decaying wood
Authors: Kulichevskaya Irina S. , Kostina Lilia A. , Valášková Vendula , Rijpstra W. Irene C. , Sinninghe Damsté Jaap S. , de Boer Wietse , Dedysh Svetlana N.
Published: August 2011

Two strains of subdivision 1

Acidobacteria

, a pink-pigmented bacterium KA1T and a colourless isolate WH120T, were obtained from acidic Sphagnum peat and wood under decay by the white-rot fungus Hyploma fasciculare, respectively. Cells of these isolates were Gram-negative-staining, non-motile, short rods, which were covered by large polysaccharide capsules and occurred singly, in pairs, or in short chains. Strains KA1T and WH120T were strictly aerobic mesophiles that grew between 10 and 33 °C, with an optimum at 22–28 °C. Both isolates developed under acidic conditions, but strain WH120T was more acidophilic (pH growth range 3.5–6.4; optimum, 4.0–4.5) than strain KA1T (pH growth range 3.5–7.3; optimum , 5.0–5.5). The preferred growth substrates were sugars. In addition, the wood-derived isolate WH120T grew on oxalate, lactate and xylan, while the peat-inhabiting acidobacterium strain KA1T utilized galacturonate, glucuronate and pectin. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω8c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid. The quinone was MK-8. The DNA G+C contents of strains KA1T and WH120T were 54.1 and 51.7 mol%, respectively. Strains KA1T and WH120T displayed 97.8 % 16S rRNA gene sequence similarity to each other. The closest recognized relatives were

Acidobacterium capsulatum

and

Telmatobacter bradus

(93.4–94.3 % 16S rRNA gene sequence similarity). These species differed from strains KA1T and WH120T by their ability to grow under anoxic conditions, the absence of capsules, presence of cell motility and differing fatty acid composition. Based on these differences, the two new isolates are proposed as representing a novel genus, Acidicapsa gen. nov., and two novel species. Acidicapsa borealis gen. nov., sp. nov. is the type species for the new genus with strain KA1T ( = DSM 23886T = LMG 25897T = VKM B-2678T) as the type strain. The name Acidicapsa ligni sp. nov. is proposed for strain WH120T ( = LMG 26244T = VKM B-2677T = NCCB 100371T).
Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment
Authors: Schmidt Verena S. J. , Wenning Mareike , Scherer Siegfried
Published: August 2011

Four non-fermenting, rod-shaped, Gram-staining-negative bacterial strains, designated WCC 4512T, WS 4555, WCC 4521T and WS 4556, were isolated from raw milk and the dairy environment. Phylogenetic analyses based on 16S rRNA and groEL gene sequences demonstrated the affiliation of the four strains to two distinct clusters within the class

Sphingobacteriia

, phylum ‘

Bacteroidetes

’. Strains WCC 4512T and WS 4555 showed the highest 16S rRNA gene sequence similarity to the type strain of

S. daejeonense

(97.3 and 97.2 %, respectively), whereas strains WCC 4521T and WS 4556 were most closely related to

S. composti

LMG 23401T (97.6 % 16S rRNA gene sequence similarity). The DNA G+C contents of strains WCC 4512T and WCC 4521T were 44.2 and 39.3 mol%, respectively. The major cellular fatty acids and the presence of menaquinone MK-7 as the predominant quinone for both strains WCC 4512T and WCC 4521T supported their affiliation to the genus

Sphingobacterium

. DNA–DNA hybridization experiments between strain WCC 4512T and

S. daejeonense

LMG 23402T and between strain WCC 4521T and

S. composti

LMG 23401T revealed DNA relatedness values of 2 % (repetition, 3 %) and 8 % (repetition, 17 %), respectively. On the basis of phenotypic and genetic properties, as well as phylogenetic distinctiveness, it is suggested that the four strains represent two novel

Sphingobacterium

species with strain WCC 4512T ( = DSM 22361T = LMG 25272T) as the type strain of Sphingobacterium lactis sp. nov. (WS 4555 is a reference strain of S. lactis) and strain WCC 4521T ( = DSM 22362T = LMG 25273T) as the type strain of Sphingobacterium alimentarium sp. nov. (WS 4556 is a reference strain of S. alimentarium).
Candida amazonensis sp. nov., an ascomycetous yeast isolated from rotting wood in the Amazonian forest
Authors: Cadete Raquel M. , Melo Monaliza A. , Lopes Mariana R. , Pereira Gilmara M. D. , Zilli Jerri E. , Vital Marcos J. S. , Gomes Fátima C. O. , Lachance Marc-André , Rosa Carlos A.
Published: August 2011

Five strains of a novel yeast species were isolated from rotting wood samples collected in an Amazonian forest site in the state of Roraima, northern Brazil. The sequences of the D1/D2 domains of the large subunit of the rRNA gene showed that this species belongs to the Scheffersomyces clade and is related to Candida coipomoensis, Candida lignicola and Candida queiroziae. The novel species Candida amazonensis sp. nov. is proposed to accommodate these isolates. The type strain of C. amazonensis sp. nov. is UFMG-HMD-26.3T ( = CBS 12363T = NRRL Y-48762T).
E‐learning in LIS education: an analysis and prediction
Authors: Islam Shiful , Kunifuji Susumu , Hayama Tessai , Miura Motoki
Published: August 2011

Purpose

The purpose of this paper is to analyze the significant factors which encourage and motivate the library and information science (LIS) academics to respond to and embrace e‐learning (EL), to explore how EL tools and technologies support the LIS education process, and to measure weights of factors constraining the use of EL in LIS education. It also reports perceptions of how LIS academics manage EL‐knowledge resources, the problems they face in managing those resources, the ways to solve those problems, and their predictions about future usage of EL in LIS education.

Design/methodology/approach

The methodology includes a combination of quantitative and qualitative methods. The authors used an exploratory online e‐mail interview method to gather experiences and data from LIS academics worldwide. The authors also used (www.docs.google.com) to prepare a questionnaire, and sent a link to the questionnaire to 85 LIS academics globally to gather their perceptions regarding EL in LIS schools.

Findings

The findings confirmed that EL overcomes location and time constraints, provides opportunities for employed and/or busy people, etc. is a driving force in education, which encourages and motivates LIS academics to respond to and embrace EL in LIS education, and EL accelerates accessibility of a wide range of knowledge, supports the process of exchanging knowledge, and increases knowledge storage capacity to enhance the LIS education process. This paper concludes that the respondents hold highly positive perceptions regarding the future of EL in LIS schools.

Originality/value

The paper explores the original perceptions of LIS academics, and their predictions regarding future usage of EL in LIS schools.
Crisis of professionalism in public services
Authors: McGuigan Glenn S.
Published: August 2011

Purpose

The purpose of this paper is to address dimensions of crisis as applied to the profession of librarianship from a public administration frame of reference. For librarians to retain professional status, the human element of librarianship must be promoted through an emphasis on their educational mission, inspired by public administration's professional code of ethics. Within this process, librarians must promote themselves as educators, embracing the concept of information literacy as their field of jurisdiction.

Design/methodology/approach

Reflecting an interdisciplinary approach, literature from public administration and library science is used to support these points.

Findings

A robust professional education and affiliation with professional associations reinforces the informational asymmetries of professionals through specialized instruction and knowledge sharing, which will lead to not only a strengthened profession, but also to opportunities for leadership.

Practical implications

To reinforce professionalism, the human element of librarianship must be promoted through an enhanced emphasis on the educational mission of librarians within the ethical framework of the profession. The place for this to occur is within schools of graduate education and professional associations.

Originality/value

This discussion addresses dimensions of crisis as applied to the profession of librarianship from a public administration frame of reference. The rationale for this approach is that library and information science can benefit from elements of the public administration school of thought regarding professionalism, in general, and ethical codes, in particular.