bluuebunny/crossref_metadata_2025 huggingface dataset:
In vacuo measurement of the sensitivity limit of planar Bragg grating sensors for monolayer detection
Authors: Parker Richard M. , Gates James C. , Grossel Martin C. , Smith Peter G. R.
Published: October 2009

An exposed Bragg grating incorporated into a planar waveguide was used to form an optical device that acts as a refractive index sensor. The exposed evanescent field causes the Bragg peak to be sensitive to the refractive index of its surroundings. The corresponding shift in peak wavelength can be used to detect changes in this environment. Incorporation of a high index overlayer onto the surface has been shown to dramatically enhance this sensitivity. The sensitivity limit was measured via the deposition of a thin film of silica, demonstrating that the system can measure down to a single surface monolayer.
Constrained-pairing mean-field theory. II. Exact treatment of dissociations to nondegenerate orbitals
Authors: Scuseria Gustavo E. , Tsuchimochi Takashi
Published: October 2009

Our recently proposed constrained-pairing mean-field theory (CPMFT) is here extended to deal with dissociation of electron pairs to nondegenerate orbitals. To achieve this goal, we introduce the concept of asymptotic constraints. This extended CPMFT model can exactly dissociate polyatomic molecules to restricted open-shell atoms or fragments. We present benchmarks showing how CPMFT accounts for static correlation in an accurate yet computationally inexpensive mean-field manner, while preserving space and spin symmetries. The key element of our approach is the admittance of electron number fluctuations into the wave function.
Magnetic multipole induced zero-rotation frequency bounce-resonant loss in a Penning–Malmberg trap used for antihydrogen trapping
Authors: Andresen G. B. , Bertsche W. , Bray C. C. , Butler E. , Cesar C. L. , Chapman S. , Charlton M. , Fajans J. , Fujiwara M. C. , Gill D. R. , Hardy W. N. , Hayano R. S. , Hayden M. E. , Humphries A. J. , Hydomako R. , Jørgensen L. V. , Kerrigan S. J. , Keller J. , Kurchaninov L. , Lambo R. , Madsen N. , Nolan P. , Olchanski K. , Olin A. , Povilus A. , Pusa P. , Robicheaux F. , Sarid E. , El Nasr S. Seif , Silveira D. M. , Storey J. W. , Thompson R. I. , van der Werf D. P. , Wurtele J. S. , Yamazaki Y. ,   ALPHA Collaboration
Published: October 2009

In many antihydrogen trapping schemes, antiprotons held in a short-well Penning–Malmberg trap are released into a longer well. This process necessarily causes the bounce-averaged rotation frequency Ω¯r of the antiprotons around the trap axis to pass through zero. In the presence of a transverse magnetic multipole, experiments and simulations show that many antiprotons (over 30% in some cases) can be lost to a hitherto unidentified bounce-resonant process when Ω¯r is close to zero.
Vibrational spectroscopy of neutral silicon clusters via far-IR-VUV two color ionization
Authors: Fielicke André , Lyon Jonathan T. , Haertelt Marko , Meijer Gerard , Claes Pieterjan , de Haeck Jorg , Lievens Peter
Published: November 2009

Tunable far-infrared-vacuum-ultraviolet two color ionization is used to obtain vibrational spectra of neutral silicon clusters in the gas phase. Upon excitation with tunable infrared light prior to irradiation with UV photons we observe strong enhancements in the mass spectrometric signal of specific cluster sizes. This allowed the recording of the infrared absorption spectra of Si6, Si7, and Si10. Structural assignments were made by comparison with calculated linear absorption spectra from quantum chemical theory.
Synaptic scaffolding protein SYD-2 clusters and activates kinesin-3 UNC-104 in C. elegans
Authors: Wagner Oliver I. , Esposito Alessandro , Köhler Barbara , Chen Chih-Wei , Shen Che-Piao , Wu Gong-Her , Butkevich Eugenia , Mandalapu Sailaja , Wenzel Dirk , Wouters Fred S. , Klopfenstein Dieter R.
Published: October 2009

Kinesin-3 motor UNC-104/KIF1A is essential for transporting synaptic precursors to synapses. Although the mechanism of cargo binding is well understood, little is known how motor activity is regulated. We mapped functional interaction domains between SYD-2 and UNC-104 by using yeast 2-hybrid and pull-down assays and by using FRET/fluorescence lifetime imaging microscopy to image the binding of SYD-2 to UNC-104 in living
Caenorhabditis elegans
. We found that UNC-104 forms SYD-2-dependent axonal clusters (appearing during the transition from L2 to L3 larval stages), which behave in FRAP experiments as dynamic aggregates. High-resolution microscopy reveals that these clusters contain UNC-104 and synaptic precursors (synaptobrevin-1). Analysis of motor motility indicates bi-directional movement of UNC-104, whereas in
syd-2
mutants, loss of SYD-2 binding reduces net anterograde movement and velocity (similar after deleting UNC-104's liprin-binding domain), switching to retrograde transport characteristics when no role of SYD-2 on dynein and conventional kinesin UNC-116 motility was found. These data present a kinesin scaffolding protein that controls both motor clustering along axons and motor motility, resulting in reduced cargo transport efficiency upon loss of interaction.
Dynamic bookmarking of primary response genes by p300 and RNA polymerase II complexes
Authors: Byun Jung S. , Wong Madeline M. , Cui Wenwu , Idelman Gila , Li Quentin , De Siervi Adriana , Bilke Sven , Haggerty Cynthia M. , Player Audrey , Wang Yong Hong , Thirman Michael J. , Kaberlein Joseph J. , Petrovas Constantinos , Koup Richard A. , Longo Dan , Ozato Keiko , Gardner Kevin
Published: October 2009

Profiling the dynamic interaction of p300 with proximal promoters of human T cells identified a class of genes that rapidly coassemble p300 and RNA polymerase II (pol II) following mitogen stimulation. Several of these p300 targets are immediate early genes, including
FOS
, implicating a prominent role for p300 in the control of primary genetic responses. The recruitment of p300 and pol II rapidly transitions to the assembly of several elongation factors, including the positive transcriptional elongation factor (P-TEFb), the bromodomain-containing protein (BRD4), and the elongin-like eleven nineteen lysine-rich leukemia protein (ELL). However, transcription at many of these rapidly induced genes is transient, wherein swift departure of P-TEFb, BRD4, and ELL coincides with termination of transcriptional elongation. Unexpectedly, both p300 and pol II remain accumulated or “bookmarked” at the proximal promoter long after transcription has terminated, demarking a clear mechanistic separation between the recruitment and elongation phases of transcription in vivo. The bookmarked pol II is depleted of both serine-2 and serine-5 phosphorylation of its C-terminal domain and remains proximally positioned at the promoter for hours. Surprisingly, these p300/pol II bookmarked genes can be readily reactivated, and elongation factors can be reassembled by subsequent addition of nonmitogenic agents that, alone, have minimal effects on transcription in the absence of prior preconditioning by mitogen stimulation. These findings suggest that p300 is likely to play an important role in biological processes in which transcriptional bookmarking or preconditioning influences cellular growth and development through the dynamic priming of genes for response to rechallenge by secondary stimuli.
Propulsion of African trypanosomes is driven by bihelical waves with alternating chirality separated by kinks
Authors: Rodríguez Jose A. , Lopez Miguel A. , Thayer Michelle C. , Zhao Yunzhe , Oberholzer Michael , Chang Donald D. , Kisalu Neville K. , Penichet Manuel L. , Helguera Gustavo , Bruinsma Robijn , Hill Kent L. , Miao Jianwei
Published: October 2009

Trypanosoma brucei
, a parasitic protist with a single flagellum, is the causative agent of African sleeping sickness. Propulsion of
T. brucei
was long believed to be by a drill-like, helical motion. Using millisecond differential interference-contrast microscopy and analyzing image sequences of cultured procyclic-form and bloodstream-form parasites, as well as bloodstream-form cells in infected mouse blood, we find that, instead, motility of
T. brucei
is by the propagation of kinks, separating left-handed and right-handed helical waves. Kink-driven motility, previously encountered in prokaryotes, permits
T. brucei
a helical propagation mechanism while avoiding the large viscous drag associated with a net rotation of the broad end of its tapering body. Our study demonstrates that millisecond differential interference-contrast microscopy can be a useful tool for uncovering important short-time features of microorganism locomotion.
A key role for vesicles in fungal secondary metabolism
Authors: Chanda Anindya , Roze Ludmila V. , Kang Suil , Artymovich Katherine A. , Hicks Glenn R. , Raikhel Natasha V. , Calvo Ana M. , Linz John E.
Published: November 2009

Eukaryotes have evolved highly conserved vesicle transport machinery to deliver proteins to the vacuole. In this study we show that the filamentous fungus
Aspergillus parasiticus
employs this delivery system to perform new cellular functions, the synthesis, compartmentalization, and export of aflatoxin; this secondary metabolite is one of the most potent naturally occurring carcinogens known. Here we show that a highly pure vesicle-vacuole fraction isolated from
A. parasiticus
under aflatoxin-inducing conditions converts sterigmatocystin, a late intermediate in aflatoxin synthesis, to aflatoxin B
1
; these organelles also compartmentalize aflatoxin. The role of vesicles in aflatoxin biosynthesis and export was confirmed by blocking vesicle-vacuole fusion using 2 independent approaches. Disruption of
A. parasiticus vb1
(encodes a protein homolog of AvaA, a small GTPase known to regulate vesicle fusion in
A. nidulans
) or treatment with Sortin3 (blocks Vps16 function, one protein in the class C tethering complex) increased aflatoxin synthesis and export but did not affect aflatoxin gene expression, demonstrating that vesicles and not vacuoles are primarily involved in toxin synthesis and export. We also observed that development of aflatoxigenic vesicles (aflatoxisomes) is strongly enhanced under aflatoxin-inducing growth conditions. Coordination of aflatoxisome development with aflatoxin gene expression is at least in part mediated by
Velvet
(VeA), a global regulator of
Aspergillus
secondary metabolism. We propose a unique 2-branch model to illustrate the proposed role for VeA in regulation of aflatoxisome development and aflatoxin gene expression.
Ultra-sensitive vibrational spectroscopy of protein monolayers with plasmonic nanoantenna arrays
Authors: Adato Ronen , Yanik Ahmet A. , Amsden Jason J. , Kaplan David L. , Omenetto Fiorenzo G. , Hong Mi K. , Erramilli Shyamsunder , Altug Hatice
Published: October 2009

Infrared absorption spectroscopy enabling direct access to vibrational fingerprints of the molecular structure is a powerful method for functional studies of bio-molecules. Although the intrinsic absorption cross-sections of IR active modes of proteins are nearly 10 orders of magnitude larger than the corresponding Raman cross-sections, they are still small compared to that of fluorescence-label based methods. Here, we developed a new tool based on collective excitation of plasmonic nanoantenna arrays and demonstrated direct detection of vibrational signatures of single protein monolayers. We first tailored the geometry of individual nanoantennas to form resonant structures that match the molecular vibrational modes. The tailored nanoantennas are then arranged in such a way that their in-phase dipolar coupling leads to a collective excitation of the ensemble with strongly enhanced near fields. The combined collective and individual plasmonic responses of the antenna array play a critical role in attaining signal enhancement factors of 10
4
–10
5
. We achieved measurement of the vibrational spectra of proteins at zeptomole levels for the entire array, corresponding to only 145 molecules per antenna. The near-field nature of the plasmonic enhancement of the absorption signals is demonstrated with progressive loading of the nanoantennas with varying protein film thicknesses. Finally, an advanced model based on nonequilibrium Green's function formalism is introduced, which explains the observed Fano-type absorption line-shapes and tuning of the absorption strengths with the antenna resonance.
Functional genomic screens identify CINP as a genome maintenance protein
Authors: Lovejoy Courtney A. , Xu Xin , Bansbach Carol E. , Glick Gloria G. , Zhao Runxiang , Ye Fei , Sirbu Bianca M. , Titus Laura C. , Shyr Yu , Cortez David
Published: November 2009

The DNA damage response (DDR) has a critical role in maintaining genome integrity and serves as a barrier to tumorigenesis by promoting cell-cycle arrest, DNA repair, and apoptosis. The DDR is activated not only by genotoxic agents that induce DNA damage, but also during aberrant cell-division cycles caused by activated oncogenes and inactivated tumor suppressors. Here we use RNAi and cDNA overexpression screens in human cells to identify genes that, when deregulated, lead to activation of the DDR. The RNAi screen identified 73 genes that, when silenced in at least two cell types, cause DDR activation. Silencing several of these genes also caused an increased frequency of micronuclei, a marker of genetically unstable cells. The cDNA screen identified 97 genes that when overexpressed induce DDR activation in the absence of any exogenous genotoxic agent, with an overrepresentation of genes linked to cancer. Secondary RNAi screens identified CDK2-interacting protein (CINP) as a cell-cycle checkpoint protein. CINP interacts with ATR-interacting protein and regulates ATR-dependent signaling, resistance to replication stress, and G2 checkpoint integrity.
Crystal structures of the noncatalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor
Authors: Akiyama Masashi , Takeda Soichi , Kokame Koichi , Takagi Junichi , Miyata Toshiyuki
Published: October 2009

ADAMTS13 specifically cleaves plasma von Willebrand factor (VWF) and thereby controls VWF-mediated platelet thrombus formation. Severe deficiencies in ADAMTS13 can cause life-threatening thrombotic thrombocytopenic purpura. Here, we determined 2 crystal structures of ADAMTS13-DTCS (residues 287–685), an exosite-containing human ADAMTS13 fragment, at 2.6-Å and 2.8-Å resolution. The structures revealed folding similarities between the disintegrin-like (D) domain and the N-terminal portion of the cysteine-rich domain (designated the C
A
domain). The spacer (S) domain forms a globular functional unit with a 10-stranded β-sandwich fold that has multiple interaction sites with the C
A
domain. We expressed 25 structure-based mutants of ADAMTS13-MDTCS (residues 75–685) and measured their enzymatic activity. We identified 3 VWF-binding exosites on the linearly aligned discontinuous surfaces of the D, C
A
, and S domains traversing the W-shaped molecule. Since the MDTCS domains are conserved among ADAMTS family proteins, the structural framework of the multiple enzyme-substrate interactions identified in the ADAMTS13-VWF system provides the basis for a common substrate recognition mode in this class of proteinases.
Stability of muscle synergies for voluntary actions after cortical stroke in humans
Authors: Cheung Vincent C. K. , Piron Lamberto , Agostini Michela , Silvoni Stefano , Turolla Andrea , Bizzi Emilio
Published: October 2009

Production of voluntary movements relies critically on the functional integration of several motor cortical areas, such as the primary motor cortex, and the spinal circuitries. Surprisingly, after almost 40 years of research, how the motor cortices specify descending neural signals destined for the downstream interneurons and motoneurons has remained elusive. In light of the many recent experimental demonstrations that the motor system may coordinate muscle activations through a linear combination of muscle synergies, we hypothesize that the motor cortices may function to select and activate fixed muscle synergies specified by the spinal or brainstem networks. To test this hypothesis, we recorded electromyograms (EMGs) from 12–16 upper arm and shoulder muscles from both the unaffected and the stroke-affected arms of stroke patients having moderate-to-severe unilateral ischemic lesions in the frontal motor cortical areas. Analyses of EMGs using a nonnegative matrix factorization algorithm revealed that in seven of eight patients the muscular compositions of the synergies for both the unaffected and the affected arms were strikingly similar to each other despite differences in motor performance between the arms, and differences in cerebral lesion sizes and locations between patients. This robustness of muscle synergies that we observed supports the notion that descending cortical signals represent neuronal drives that select, activate, and flexibly combine muscle synergies specified by networks in the spinal cord and/or brainstem. Our conclusion also suggests an approach to stroke rehabilitation by focusing on those synergies with altered activations after stroke.
Caterpillars did not evolve from onychophorans by hybridogenesis
Authors: Hart Michael W. , Grosberg Richard K.
Published: October 2009

The evolution and loss of distinctive larval forms in animal life cycles have produced complex patterns of similarity and difference among life-history stages and major animal lineages. One example of this similarity is the morphological forms of Onychophora (velvet worms) and the caterpillar-like larvae of some insects. Williamson [(2009)
Proc Natl Acad Sci USA
106:15786–15790] has made the astonishing and unfounded claim that the ancestors of the velvet worms directly gave rise to insect caterpillars via hybridization and that evidence of this ancient “larval transfer” could be found in comparisons among the genomes of extant onychophorans, insects with larvae, and insects without larvae. Williamson has made a series of predictions arising from his hypothesis and urged genomicists to test them. Here, we use data already in the literature to show these predictions to be false. Hybridogenesis between distantly related animals does not explain patterns of morphological and life-history evolution in general, and the genes and genomes of animals provide strong evidence against hybridization or larval transfer between a velvet worm and an insect in particular.
Language patterns and ATTITUDE
Authors: Bednarek Monika
Published: October 2009

Interpersonal or evaluative meaning has been described in systemic functional linguistics with the help of appraisal theory (Martin & White 2005), which distinguishes between different types of evaluation. One sub-system of APPRAISAL is ATTITUDE, which is further divided into APPRECIATION, JUDGEMENT and AFFECT. This paper uses corpus-linguistic evidence to investigate how far linguistic patterns support this classification, and whether they can be used as a ‘diagnostic’ for distinguishing types of ATTITUDE (as has been proposed in appraisal theory). It argues that two different aspects of APPRAISAL need to be considered: the kinds of attitudinal lexis (in terms of evaluative standards which are inscribed in this lexis) and the kinds of attitudinal targets or types of attitudinal assessment, and that this distinction has not been sufficiently considered in appraisal theory so far. A preliminary classification of attitudinal lexis is also suggested, and a new sub-category of ATTITUDE proposed (COVERT AFFECT).
Knowledge moves in conversational exchanges
Authors: Muntigl Peter
Published: October 2009

In Berry’s (1981) classic work on exchange structure, it was argued that knowledge exchanges consist of some conversational participant who already knows the information and some conversational participant to whom the information is imparted. The former participant is commonly termed the primary knower, whereas the latter is termed the secondary knower. What is missing in Berry’s model (and work that has extended Berry’s model), however, is (1) an explanation of how rights and access to knowledge can be claimed or resisted on a turn-by-turn and move-by-move basis, and (2) a more elaborated conception of knowledge that goes beyond a sender/receiver model of information. Drawing from a corpus of spoken conversation from diverse sources, I extend Berry’s model by showing how a participant’s ‘knower status’ is often negotiated within an exchange. As an interpersonal resource, knowledge can be asserted, challenged, resisted, accepted, expanded, upgraded, downgraded, etc. Furthermore, I argue that ‘knowledge’ should be given a social/practical epistemological interpretation; from this perspective, knowledge is associated with a speaker’s degree of access to information and with a speaker’s rights and obligations to know.
Pointing the Yoruba way
Authors: Orie Ọlanikẹ Ọla
Published: October 2009

This paper gives a description of Yoruba pointing behavior, especially pointing as it relates to people in interaction contexts. First, it is shown that pointing is regulated by socio-cultural factors. Secondly, it is shown that non-manual points such as lip points are complex points which use the gaze as the primary pointer; other head-area gestures ‘switch on’ the deictic function of the gaze to pinpoint the specific referent in the discourse space. This paper also describes a form of pointing, termed ‘eye-click’, in which the eyes have both the function of gazing and ‘switching on’ the deictic vector of gaze. Thirdly, some pointing practices in sub-Saharan Africa are examined and compared.
Semantic niches and analogy in word formation
Authors: Hüning Matthias
Published: October 2009

Word formation, like other lexical phenomena, seems to be a difficult terrain for contrastive linguistics since it hardly allows for significant and insightful generalizations about the differences between two languages, as has been stated in the literature more than once. This paper investigates one factor leading to morphological differences and contrasts between historically related languages (Dutch and German). It is argued that word formation processes often show semantic fragmentation: in the course of time they develop ‘semantic niches’, i.e. groups of words (subsets of a morphological category) kept together by formal and semantic criteria and extendable via analogy. When looking at word formation from a contrastive point of view, these niches seem to allow for better generalizations in terms of systematic correspondences and differences between two languages than the category as a whole. As a consequence, productivity should not be seen as an absolute notion, but rather as a local and gradual phenomenon. Morphology should not only account for the possibility of coining new words but also for their probability, because language comparison shows that even allegedly equivalent word formation processes often differ with respect to the probability of their use. The paper therefore argues in favour of an analogy approach that takes the existence of semantic niches seriously.
Plasmon dispersion of low-frequency oscillations in metallic double-walled carbon nanotubes
Authors: Fathalian Ali , Nikjo Shahram
Published: November 2009

The dispersion properties of low-frequency electromagnetic waves in metallic double-walled carbon nanotubes (DWCNTs) are investigated. We assume that metallic DWCNTs are charged due to field emission, and hence metallic nanotubes can be regarded as charged dust rods surrounded by degenerate electrons and ions. Calculations are performed for transverse magnetic (TM) and transverse electric (TE) waves, respectively, by solving Maxwell and hydrodynamic equations with appropriate boundary conditions.
Predictive rule inference for epistatic interaction detection in genome-wide association studies
Authors: Wan Xiang , Yang Can , Yang Qiang , Xue Hong , Tang Nelson L.S. , Yu Weichuan
Published: October 2009

Motivation: Under the current era of genome-wide association study (GWAS), finding epistatic interactions in the large volume of SNP data is a challenging and unsolved issue. Few of previous studies could handle genome-wide data due to the difficulties in searching the combinatorially explosive search space and statistically evaluating high-order epistatic interactions given the limited number of samples. In this work, we propose a novel learning approach (SNPRuler) based on the predictive rule inference to find disease-associated epistatic interactions.

Results: Our extensive experiments on both simulated data and real genome-wide data from Wellcome Trust Case Control Consortium (WTCCC) show that SNPRuler significantly outperforms its recent competitor. To our knowledge, SNPRuler is the first method that guarantees to find the epistatic interactions without exhaustive search. Our results indicate that finding epistatic interactions in GWAS is computationally attainable in practice.

Availability:  http://bioinformatics.ust.hk/SNPRuler.zip

Contact:  eexiangw@ust.hk, eeyu@ust.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Centella asiatica Improves Physical Performance and Health‐Related Quality of Life in Healthy Elderly Volunteer
Authors: Mato Lugkana , Wattanathorn Jintanaporn , Muchimapura Supaporn , Tongun Terdthai , Piyawatkul Nawanant , Yimtae Kwanchanok , Thanawirattananit Panida , Sripanidkulchai Bungorn
Published: October 2009

Recently, oxidative stress has been reported to contribute an important role in the decline of physical function as age advances. Numerous antioxidants can improve both physical and psychological performances resulting in the increase of health‐related quality of life (HQOL). Therefore, we hypothesized that Centella asiatica, a medicinal plant reputed for nerve tonic, strength improvement and antioxidant activity, could improve the physical performance and HQOL especially in the physical satisfaction aspect, of the healthy elderly volunteer. To test this hypothesis, a double‐blind, placebo‐controlled, randomized trial was performed. Eighty healthy elderly were randomly assigned to receive placebo or standardized extract of C. asiatica at doses of 250, 500 and 750 mg once daily for 90 days. The subjects were evaluated to establish baseline data of physical performance using 30‐s chair stand test, hand grip test and 6‐min walk test. The health‐related quality of life was assessed using SF‐36. These assessments were repeated every month throughout the 3‐month experimental period using the aforementioned parameters. Moreover, 1 month after the cessation of C. asiatica treatment, all subjects were also evaluated using these parameters again. The results showed that after 2 months of treatment, C. asiatica at doses of 500 and 750 mg per day increased lower extremity strength assessed via the 30‐s chair stand test. In addition, the higher doses of C. asiatica could improve the life satisfaction subscale within the physical function subscale. Therefore, the results from this study appear to support the traditional reputation of C. asiatica on strength improvement, especially in the lower extremities of the elderly. C. asiatica also possesses the potential to be a natural resource for vigor and strength increase, in healthy elderly persons. However, further research is essential.
Hypolipidemic Effects of Three Purgative Decoctions
Authors: Tseng Sung-Hui , Chien Ting-Yi , Chen Jiun-Rong , Lin I-Hsin , Wang Ching-Chiung
Published: October 2009

In traditional Chinese medicine (TCM), purgation is indicated when a person suffers an illness due to the accumulation of evil internal heat. Obese individuals with a large belly, red face, thick and yellow tongue fur, constipation, and avoidance of heat are thought accumulates of evil internal heat, and they are also treated with purgatives such as Ta-Cheng-Chi-Tang (TCCT), Xiao-Chen-Chi-Tang (XCCT), and Tiao-Wei-Chen-Chi-Tang (TWCCT) by TCM doctors. In previous studies, our group found that TCCT has potent anti‐inflammatory activity, and that XCCT is an effective antioxidant. Since rhubarb is the principle herb in these three prescriptions, we will first present a thorough review of the literature on the demonstrated effect (or lack of effect) of rhubarb and rhubarb‐containing polyherbal preparations on lipid and weight control. We will then continue our research with an investigation of the anti‐obesity and lipid‐lowering effect of TCCT, XCCT, TWCCT, and rhubarb extracts using two animal models. TWCCT lowered the serum triglyceride concentration as much as fenofibrate in Triton WR‐1339‐treated mice. Daily supplementation with XCCT and TWCCT significantly attenuated the high‐fat‐diet‐induced hypercholesterolemia in rats. In addition, TWCCT also significantly lowered the high‐fat‐diet‐induced hypertriglycemia. Although feeding high‐fat diet rats with these extracts did not cause loose stools or diarrhea or other deleterious effects on renal or hepatic function. None of these extracts lowered the body weight of rats fed on high‐fat diet. In conclusion, the results suggest that XCCT and TWCCT might exert beneficial effects in the treatment of hyperlipidemia.
Comments on Comments, or the Richness of Dialogue
Authors: Godelier Eric
Published: November 2009

If my initial essay at a minimum had the objective of generating a debate and fruitful exchanges, it has succeeded. Of course, probably because of the inevitable ambiguities of translation, some of Chris Kobrak's, Andrew Popp's, and Paul Tiffany's comments suggest that a few further remarks are in order to clarify a set of ideas and allow further developments or discussions.
Fishing simulation experiments for predicting the effects of purse-seine capture on sardine (Sardina pilchardus)
Authors: Marçalo Ana , Marques Tiago A. , Araújo João , Pousão-Ferreira Pedro , Erzini Karim , Stratoudakis Yorgos
Published: November 2009

Marçalo, A., Marques, T. A., Araújo, J., Pousão-Ferreira, P., Erzini, K., and Stratoudakis, Y. 2010. Fishing simulation experiments for predicting the effects of purse-seine capture on sardine (Sardina pilchardus). – ICES Journal of Marine Science, 67: 334–344. To study the impact of purse-seine fishing on deliberately released sardine, two laboratory experiments were performed to explore the effect of net confinement for 10, 20, 40, and 60 min at 18 and 23°C. A third experiment considered two levels of fish density while confined for 20 and 40 min at 16°C. Analysis of cortisol and haematocrit demonstrated that stress immediately after simulated fishing was milder than in commercial fishing and did not correlate with observed delayed mortality. Scale loss was related to the probability of dying (mean values of 16.3 and 2% for dead fish and survivors, respectively), and fin erosion was a long-term stress response observed in both dead and surviving fish. Time of confinement was an important stressor, with survival rates decreasing significantly with increasing periods in the net, and temperature having an additional negative effect. Density effects were less conclusive, but there was some indication that survival correlated with biological condition (heavier fish were more likely to survive). It seems that delayed mortality after release can be substantial, although death is not certain and appropriately modified fishing operations and favourable environmental conditions may enhance the probability of sardine survival.
Amycolatopsis xylanica sp. nov., isolated from soil
Authors: Chen Jie , Su Jin-Jin , Wei Yu-Zhen , Li Qiu-Ping , Yu Li-Yan , Liu Hong-Yu , Zhang Yu-Qin , Zhang Yue-Qin
Published: October 2009

An actinomycete, designated CPCC 202699T, was isolated from soil in Qinghai province, China, and its taxonomic status was established. Strain CPCC 202699Tcontainedmeso-diaminopimelic acid in its peptidoglycan, arabinose and galactose as the diagnostic sugars in whole-cell hydrolysates, a phospholipid pattern consisting mainly of phosphatidylethanolamine, phosphatidylmethylethanolamine and phosphatidylcholine, MK-9(H4) as the predominant menaquinone and iso-C16 : 0(18.8 %), iso-C15 : 0(18.1 %), iso-C14 : 0(14.2 %), C16 : 1cis9 (10.9 %) and C17 : 1cis9 (10.3 %) as the major fatty acids. In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 202699Tformed a separate branch within the genusAmycolatopsis. However, strain CPCC 202699Tshowed low 16S rRNA gene sequence similarities (<97.0 %) with type strains of species with validly published names in the genusAmycolatopsis. On the basis of genotypic and phenotypic differences from the closest phylogenetic neighbours of strain CPCC 202699T, a novel species,Amycolatopsis xylanicasp. nov., is proposed. The type strain is CPCC 202699T(=DSM 45285T=KCTC 19581T=CCM 7627T).
Marmoricola scoriae sp. nov., isolated from volcanic ash
Authors: Lee Dong Wan , Lee Soon Dong
Published: October 2009

A novel Gram-stain-positive, coccoid actinobacterium, designated strain Sco-D01T, was isolated from volcanic ash collected from Oreum (a parasitic volcanic cone) on Jeju Island, Republic of Korea. Cells were aerobic, oxidase-negative and catalase-positive. Colonies were vivid yellow, circular, smooth and convex. The diagnostic diamino acid in the cell wall was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unknown phospholipid. The fatty acid profile was represented by large amounts of saturated, unsaturated, 10-methyl and hydroxyl components. The DNA G+C content of strain Sco-D01T was 72.0 mol%. 16S rRNA gene sequence analysis revealed that strain Sco-D01T belonged to the family Nocardioidaceae and formed a distinct sublineage within the radiation of the genus Marmoricola. The level of DNA–DNA relatedness between strain Sco-D01T and its closest phylogenetic relative, Marmoricola aurantiacus DSM 12652T, was 30.2 % (35.4 % in duplicate measurements). On the basis of phenotypic and DNA–DNA hybridization data, strain Sco-D01T is considered to represent a novel species of the genus Marmoricola, for which the name Marmoricola scoriae sp. nov. is proposed. The type strain is Sco-D01T (=KCTC 19597T=DSM 22127T).
Haloechinothrix alba gen. nov., sp. nov., a halophilic, filamentous actinomycete of the suborder Pseudonocardineae
Authors: Tang Shu-Kun , Wang Yun , Zhang Hua , Lee Jae-Chan , Lou Kai , Kim Chang-Jin , Li Wen-Jun
Published: October 2009

A novel halophilic, filamentous actinomycete strain, designated YIM 93221T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. The isolate grew with 9–23 % (w/v) NaCl and did not grow without NaCl. The isolate formed spiny aerial mycelium and did not form spores at maturity. The isolate contained meso-diaminopimelic acid as the diagnostic diamino acid and glucose, glucosamine, mannose and an unknown sugar as the major whole-cell sugars. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and an unknown phospholipid. MK-8(H4) was the predominant menaquinone. The major fatty acid was iso-C16 : 0. The DNA G+C content was 68.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 93221T formed a distinct lineage within the suborder Pseudonocardineae and showed 91.9–94.8 % 16S rRNA gene sequence similarity with members of the suborder Pseudonocardineae. On the basis of the evidence from this polyphasic study, a novel genus and species, Haloechinothrix alba gen. nov., sp. nov., are proposed. The type strain of Haloechinothrix alba is YIM 93221T (=DSM 45207T =CCTCC AB 208140T).
Phenotypic Plasticity in Photosynthetic Temperature Acclimation among Crop Species with Different Cold Tolerances
Authors: Yamori Wataru , Noguchi Ko , Hikosaka Kouki , Terashima Ichiro
Published: October 2009

While interspecific variation in the temperature response of photosynthesis is well documented, the underlying physiological mechanisms remain unknown. Moreover, mechanisms related to species-dependent differences in photosynthetic temperature acclimation are unclear. We compared photosynthetic temperature acclimation in 11 crop species differing in their cold tolerance, which were grown at 15°C or 30°C. Cold-tolerant species exhibited a large decrease in optimum temperature for the photosynthetic rate at 360 μL L™1 CO2 concentration [Opt (A  360)] when growth temperature decreased from 30°C to 15°C, whereas cold-sensitive species were less plastic in Opt (A  360). Analysis using the C3 photosynthesis model shows that the limiting step of A  360 at the optimum temperature differed between cold-tolerant and cold-sensitive species; ribulose 1,5-bisphosphate carboxylation rate was limiting in cold-tolerant species, while ribulose 1,5-bisphosphate regeneration rate was limiting in cold-sensitive species. Alterations in parameters related to photosynthetic temperature acclimation, including the limiting step of A  360, leaf nitrogen, and Rubisco contents, were more plastic to growth temperature in cold-tolerant species than in cold-sensitive species. These plastic alterations contributed to the noted growth temperature-dependent changes in Opt (A  360) in cold-tolerant species. Consequently, cold-tolerant species were able to maintain high A  360 at 15°C or 30°C, whereas cold-sensitive species were not. We conclude that differences in the plasticity of photosynthetic parameters with respect to growth temperature were responsible for the noted interspecific differences in photosynthetic temperature acclimation between cold-tolerant and cold-sensitive species.
A Host RNA Helicase-Like Protein, AtRH8, Interacts with the Potyviral Genome-Linked Protein, VPg, Associates with the Virus Accumulation Complex, and Is Essential for Infection
Authors: Huang Tyng-Shyan , Wei Taiyun , Laliberteݩ Jean-Francࠇois , Wang Aiming
Published: October 2009

The viral genome-linked protein, VPg, of potyviruses is a multifunctional protein involved in viral genome translation and replication. Previous studies have shown that both eukaryotic translation initiation factor 4E (eIF4E) and eIF4G or their respective isoforms from the eIF4F complex, which modulates the initiation of protein translation, selectively interact with VPg and are required for potyvirus infection. Here, we report the identification of two DEAD-box RNA helicase-like proteins, PpDDXL and AtRH8 from peach (Prunus persica) and Arabidopsis (Arabidopsis thaliana), respectively, both interacting with VPg. We show that AtRH8 is dispensable for plant growth and development but necessary for potyvirus infection. In potyvirus-infected Nicotiana benthamiana leaf tissues, AtRH8 colocalizes with the chloroplast-bound virus accumulation vesicles, suggesting a possible role of AtRH8 in viral genome translation and replication. Deletion analyses of AtRH8 have identified the VPg-binding region. Comparison of this region and the corresponding region of PpDDXL suggests that they are highly conserved and share the same secondary structure. Moreover, overexpression of the VPg-binding region from either AtRH8 or PpDDXL suppresses potyvirus accumulation in infected N. benthamiana leaf tissues. Taken together, these data demonstrate that AtRH8, interacting with VPg, is a host factor required for the potyvirus infection process and that both AtRH8 and PpDDXL may be manipulated for the development of genetic resistance against potyvirus infections.
The Photosystem II Light-Harvesting Protein Lhcb3 Affects the Macrostructure of Photosystem II and the Rate of State Transitions inArabidopsis
Authors: Damkjær Jakob T. , Kereïche Sami , Johnson Matthew P. , Kovacs Laszlo , Kiss Anett Z. , Boekema Egbert J. , Ruban Alexander V. , Horton Peter , Jansson Stefan
Published: October 2009

The main trimeric light-harvesting complex of higher plants (LHCII) consists of three different Lhcb proteins (Lhcb1-3). We show that Arabidopsis thaliana T-DNA knockout plants lacking Lhcb3 (koLhcb3) compensate for the lack of Lhcb3 by producing increased amounts of Lhcb1 and Lhcb2. As in wild-type plants, LHCII-photosystem II (PSII) supercomplexes were present in Lhcb3 knockout plants (koLhcb3), and preservation of the LHCII trimers (M trimers) indicates that the Lhcb3 in M trimers has been replaced by Lhcb1 and/or Lhcb2. However, the rotational position of the M LHCII trimer was altered, suggesting that the Lhcb3 subunit affects the macrostructural arrangement of the LHCII antenna. The absence of Lhcb3 did not result in any significant alteration in PSII efficiency or qE type of nonphotochemical quenching, but the rate of transition from State 1 to State 2 was increased in koLhcb3, although the final extent of state transition was unchanged. The level of phosphorylation of LHCII was increased in the koLhcb3 plants compared with wild-type plants in both State 1 and State 2. The relative increase in phosphorylation upon transition from State 1 to State 2 was also significantly higher in koLhcb3. It is suggested that the main function of Lhcb3 is to modulate the rate of state transitions.
NO VEIN Mediates Auxin-Dependent Specification and Patterning in theArabidopsisEmbryo, Shoot, and Root
Authors: Tsugeki Ryuji , Ditengou Franck Anicet , Sumi Yoshinori , Teale William , Palme Klaus , Okada Kiyotaka
Published: October 2009

Local efflux-dependent auxin gradients and maxima mediate organ and tissue development in plants. Auxin efflux is regulated by dynamic expression and subcellular localization of the PIN auxin-efflux proteins, which appears to be established not only through a self-organizing auxin-mediated polarization mechanism, but also through other means, such as cell fate determination and auxin-independent mechanisms. Here, we show that the Arabidopsis thaliana NO VEIN (NOV) gene, encoding a novel, plant-specific nuclear factor, is required for leaf vascular development, cellular patterning and stem cell maintenance in the root meristem, as well as for cotyledon outgrowth and separation. nov mutations affect many aspects of auxin-dependent development without directly affecting auxin perception. NOV is required for provascular PIN1 expression and region-specific expression of PIN7 in leaf primordia, cell type–specific expression of PIN3, PIN4, and PIN7 in the root, and PIN2 polarity in the root cortex. NOV is specifically expressed in developing embryos, leaf primordia, and shoot and root apical meristems. Our data suggest that NOV function underlies cell fate decisions associated with auxin gradients and maxima, thus establishing cell type–specific PIN expression and polarity. We propose that NOV mediates the acquisition of competence to undergo auxin-dependent coordinated cell specification and patterning, thereby eliciting context-dependent auxin-mediated developmental responses.
Anti‐nutritional content of products developed from potato flour
Authors: Lakra Poonam , Sehgal Salil
Published: October 2009

Purpose

The purpose of this paper to standardize the technique for the development of potato flour and to incorporate it in development of the products along with defatted soy flour and maize flour. Also, effect of processing techniques like frying and fermentation on anti‐nutritional content of the products was studied.

Design/methodology/approach

The ingredients as well as developed products were analyzed for the macronutrients, viz protein, ash and fat. Also anti‐nutrients like phytic acid, saponin, polyphenols and trypsin inhibitors were estimated by employing standard techniques. Data thus obtained were subjected to analysis of variance according to standard method of statistical analysis.

Findings

Potato flour being a versatile ingredient can be easily incorporated in development of various products. Frying and fermentation resulted in decrease of anti‐nutritional factors.

Originality/value

These developed products could be instrumental in alleviating malnutrition as they have high nutritional value and are low in anti‐nutrients.
Market creation: the epitome of entrepreneurial marketing practices
Authors: Gaddefors Johan , Anderson Alistair R.
Published: October 2009

Purpose

The purpose of this paper is to examine theories of marketing and entrepreneurship and compare these with entrepreneurial marketing practices.

Design/methodology/approach

The paper uses a case study to explore the social constructions of narratives.

Findings

The paper reveals how interactions based around meanings, purpose and identities work to create products, customers, entrepreneurs and even the market. Here the emphasis on signs, symbols and images redirects attention to create space for expectations to grow.

Research limitations/implications

The paper develops its argument that merely modifying existing theory is conceptually inadequate; a new framework is introduced which enables the understanding of how entrepreneurship and marketing combine. The paper shows how this fertile dynamic produces not only new products, but also may actually create new markets.

Originality/value

This case study demonstrates how entrepreneurship and marketing become inseparable in the co‐production of identity and future.
Mecca‐Cola: message in a bottle
Authors: Justo Rachida , Cruz Cristina
Published: October 2009

Purpose

This paper aims to describe how Taoufik Mathlouthi created Mecca‐Cola, a beverage designed as an alternative to major American colas. It is intended to raise student's consciousness about the fact that good opportunities can be driven by political and social changes. Second, it aims to bring them the opportunity to reflect about their own definition of a social entrepreneur and understand the challenges behind pursuing multiple objectives that is, trying to blend and integrate non‐profit goals with rigorous venture development practices.

Design/methodology/approach

To write this case, two complementary methodologies were relied on: interviews with founder and employees and use of secondary information such as press articles.

Findings

The case describes how what began as a venture for French Muslims, garnered international appeal, with markets opening up in 54 countries in less than two years. However, despite this success, the following stage of transforming Mecca‐Cola into a sustainable business while maintaining its “essence” was proving difficult for the company.

Originality/value

The case is intended for an undergraduate or MBA course in entrepreneurship. The innovative aspect is that the entrepreneur discovered a business opportunity that arose in the wake of the Iraq war in the form of discontent with US foreign policy among some sectors of the population. As courses on social entrepreneurship begin to emerge in academic institutions this case also offers an interesting example of the challenges brought about initiating this kind of business and achieving a double bottom line.