bluuebunny/crossref_metadata_2025 huggingface dataset:
VEGF-B promotes cancer metastasis through a VEGF-A–independent mechanism and serves as a marker of poor prognosis for cancer patients
Authors: Yang Xiaojuan , Zhang Yin , Hosaka Kayoko , Andersson Patrik , Wang Jian , Tholander Fredrik , Cao Ziquan , Morikawa Hiromasa , Tegnér Jesper , Yang Yunlong , Iwamoto Hideki , Lim Sharon , Cao Yihai
Published: May 2015

Significance

Cancer metastasis is responsible for a majority of the mortality in cancer patients and involves complex interactions, modulated by various factors and cytokines, between malignant and host cells. Vascular structures in solid tumors are crucial for cancer cell intravasation into the circulation. Our present work shows that VEGF-B produced by tumor cells significantly remodels tumor microvasculature, leading to leaky vascular networks that are highly permissive for tumor cell invasion. VEGF-B–promoted cancer metastasis occurs through a VEGF-A–independent mechanism. Thus, inhibition of VEGF-B should be considered an independent approach for the development of new drugs for the treatment of cancer invasion and metastasis. VEGF-B also may be considered as an independent prognostic marker for cancer metastasis.
Water loss prevention plays a greater role than ROS scavenging in dehydration tolerance of Kalanchoe tubiflora epiphyllous buds
Authors: Luo Yin Ling , Su Zhi Long , Cui Xian Liang , Lan Qin Ying
Published: May 2015

Different plants and plant organs have various strategies to cope with drought stress.Kalanchoe tubifloraplants have a strong ability to prevent water loss and to scavenge reactive oxygen species. The epiphyllous bud of the plant serves as a reproduction unit and is able to generate plantlets even under conditions of extreme drought. The aim of this project was to study the antioxidant-stress response and osmoregulation ofK. tubifloraepiphyllous buds to dehydration and to compare the drought-tolerance mechanisms of the plant body and the epiphyllous buds. With the progression of bud dehydration, relative water content, seedling survival rate and dry weight per seedling decreased, and electrolyte leakage, hydrogen peroxide and malondialdehyde content and superoxide anion production rate increased. The activities of the antioxidant enzymes superoxide dismutase, catalase, ascorbate peroxidase, dehydroascorbate reductase and glutathione reductase decreased under dehydration. The content of proline, soluble sugars and soluble protein increased in dehydrated buds proportionally with the extent of water loss. These data indicate that the drought-tolerance mechanism of theK. tubiflorabud was different from that of its mother plant. The buds invest more energy to prevent water loss during drought stress, and their antioxidant defense weakens.
Cd accumulation potential as a marker for heavy metal tolerance in soybean
Authors: Socha Peter , Bernstein Nirit , Rybanský Ĺubomír , Mészáros Patrik , Gálusová Terézia , Spieß Nadine , Libantová Jana , Moravčíková Jana , Matušíková Ildikó
Published: May 2015

Plants have a potential for the uptake and accumulation of essential and non-essential trace elements. The ability to take up and tolerate metals varies between and within species as well as between metals. For most metals, the mechanisms involved in plant tolerance, uptake and accumulation are still not fully known and it is not known to what extent the plant response is metal-specific rather than a general stress response. In the present study, the growth response of soybean to Cd, As, Al and NaCl was compared and contrasted to simple sequence repeat (SSR) marker analysis results for Cda1, a dominant gene located in a major quantitative trait locus that regulates Cd accumulation in soybean, to evaluate the hypothesis that general effect patterns are induced by the individual metals. Principal component analysis revealed that the root growth response was most diverse for Al exposure and decreased in the order of Al > As > Cd > NaCl. NaCl did not exert a differentiating effect, indicating response mechanisms similar, at least partially, to metal exposure. The applied stressors yielded a distinguishable pattern of root responses, indicating the potential of such screens to identify agents acting similarly or differently. The SSR marker analysis also facilitated characterization of the Cd accumulation potential of the 22 soybean cultivars studied, and thereby identification of cultivars with potential health risk under cultivation in Cd-contaminated soils.
Ageing and Feature Binding in Visual Working Memory: The Role of Presentation Time
Authors: Rhodes Stephen , Parra Mario A. , Logie Robert H.
Published: May 2015

A large body of research has clearly demonstrated that healthy ageing is accompanied by an associative memory deficit. Older adults exhibit disproportionately poor performance on memory tasks requiring the retention of associations between items (e.g., pairs of unrelated words). In contrast to this robust deficit, older adults’ ability to form and temporarily hold bound representations of an object's surface features, such as colour and shape, appears to be relatively well preserved. However, the findings of one set of experiments suggest that older adults may struggle to form temporary bound representations in visual working memory when given more time to study objects. However, these findings were based on between-participant comparisons across experimental paradigms. The present study directly assesses the role of presentation time in the ability of younger and older adults to bind shape and colour in visual working memory using a within-participant design. We report new evidence that giving older adults longer to study memory objects does not differentially affect their immediate memory for feature combinations relative to individual features. This is in line with a growing body of research suggesting that there is no age-related impairment in immediate memory for colour-shape binding.
Numerical computations concerning the GRH
Authors: Platt David
Published: May 2015

We describe two new algorithms for the efficient and rigorous computation of Dirichlet L-functions and their use to verify the Generalised Riemann Hypothesis for all such L-functions associated with primitive characters of modulus

q
≤
400

000

q\leq 400\,000

. We check, to height,

max

(

10
8

q

,

A
⋅

10
7

q

+
200
)

\textrm {max}\left (\frac {10^8}{q},\frac {A\cdot 10^7}{q}+200\right )

with

A
=
7.5

A=7.5

in the case of even characters and

A
=
3.75

A=3.75

for odd characters. In addition we confirm that no Dirichlet L-function with a modulus

q
≤
2

000

000

q\leq 2\,000\,000

vanishes at its central point.
Remarks on absolute continuity in the context of free probability and random matrices
Authors: Chakrabarty Arijit , Hazra Rajat
Published: May 2015

In this note, we show that the limiting spectral distribution of symmetric random matrices with stationary entries is absolutely continuous under some sufficient conditions. This result is applied to obtain sufficient conditions on a probability measure for its free multiplicative convolution with the semicircle law to be absolutely continuous.
Davies type estimate and the heat kernel bound under the Ricci flow
Authors: Zhu Meng
Published: May 2015

We prove a Davies type double integral estimate for the heat kernel

H
(
y
,
t
;
x
,
l
)

H(y,t;x,l)

under the Ricci flow. As a result, we give an affirmative answer to a question proposed by Chow et al. Moreover, we apply the Davies type estimate to provide a new proof of the Gaussian upper and lower bounds of

H
(
y
,
t
;
x
,
l
)

H(y,t;x,l)

which were first shown in 2011 by Chan, Tam, and Yu.
DSigDB: drug signatures database for gene set analysis
Authors: Yoo Minjae , Shin Jimin , Kim Jihye , Ryall Karen A. , Lee Kyubum , Lee Sunwon , Jeon Minji , Kang Jaewoo , Tan Aik Choon
Published: May 2015

Summary: We report the creation of Drug Signatures Database (DSigDB), a new gene set resource that relates drugs/compounds and their target genes, for gene set enrichment analysis (GSEA). DSigDB currently holds 22 527 gene sets, consists of 17 389 unique compounds covering 19 531 genes. We also developed an online DSigDB resource that allows users to search, view and download drugs/compounds and gene sets. DSigDB gene sets provide seamless integration to GSEA software for linking gene expressions with drugs/compounds for drug repurposing and translational research.

Availability and implementation: DSigDB is freely available for non-commercial use at http://tanlab.ucdenver.edu/DSigDB.

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  aikchoon.tan@ucdenver.edu
Host age modulates within-host parasite competition
Authors: Izhar Rony , Routtu Jarkko , Ben-Ami Frida
Published: May 2015

In many host populations, one of the most striking differences among hosts is their age. While parasite prevalence differences in relation to host age are well known, little is known on how host age impacts ecological and evolutionary dynamics of diseases. Using two clones of the water flea
Daphnia magna
and two clones of its bacterial parasite
Pasteuria ramosa
, we examined how host age at exposure influences within-host parasite competition and virulence. We found that multiply-exposed hosts were more susceptible to infection and suffered higher mortality than singly-exposed hosts. Hosts oldest at exposure were least often infected and vice versa. Furthermore, we found that in young multiply-exposed hosts competition was weak, allowing coexistence and transmission of both parasite clones, whereas in older multiply-exposed hosts competitive exclusion was observed. Thus, age-dependent parasite exposure and host demography (age structure) could together play an important role in mediating parasite evolution. At the individual level, our results demonstrate a previously unnoticed interaction of the host's immune system with host age, suggesting that the specificity of immune function changes as hosts mature. Therefore, evolutionary models of parasite virulence might benefit from incorporating age-dependent epidemiological parameters.
Bioeconomic analysis of child-targeted subsidies for artemisinin combination therapies: a cost-effectiveness analysis
Authors: Klein Eili Y. , Smith David L. , Cohen Justin M. , Laxminarayan Ramanan
Published: May 2015

The Affordable Medicines Facility for malaria (AMFm) was conceived as a global market-based mechanism to increase access to effective malaria treatment and prolong effectiveness of artemisinin. Although results from a pilot implementation suggested that the subsidy was effective in increasing access to high-quality artemisinin combination therapies (ACTs), the Global Fund has converted AMFm into a country-driven mechanism whereby individual countries could choose to fund the subsidy from within their country envelopes. Because the initial costs of the subsidy in the pilot countries was higher than expected, countries are also exploring alternatives to a universal subsidy, such as subsidizing only child doses. We examined the incremental cost-effectiveness of a child-targeted policy using an age-structured bioeconomic model of malaria from the provider perspective. Because the vast majority of malaria deaths occur in children, targeting children could potentially improve the cost-effectiveness of the subsidy, though it would avert significantly fewer deaths. However, the benefits of a child-targeted subsidy (i.e. deaths averted) are eroded as leakage (i.e. older individuals taking young child-targeted doses) increases, with few of the benefits of a universal subsidy gained (i.e. reductions in overall prevalence). Although potentially more cost-effective, a child-targeted subsidy must contain measures to reduce the possibility of leakage.
Modulation of cell function by electric field: a high-resolution analysis
Authors: Taghian T. , Narmoneva D. A. , Kogan A. B.
Published: May 2015

Regulation of cell function by a non-thermal, physiological-level electromagnetic field has potential for vascular tissue healing therapies and advancing hybrid bioelectronic technology. We have recently demonstrated that a physiological electric field (EF) applied wirelessly can regulate intracellular signalling and cell function in a frequency-dependent manner. However, the mechanism for such regulation is not well understood. Here, we present a systematic numerical study of a cell-field interaction following cell exposure to the external EF. We use a realistic experimental environment that also recapitulates the absence of a direct electric contact between the field-sourcing electrodes and the cells or the culture medium. We identify characteristic regimes and present their classification with respect to frequency, location, and the electrical properties of the model components. The results show a striking difference in the frequency dependence of EF penetration and cell response between cells suspended in an electrolyte and cells attached to a substrate. The EF structure in the cell is strongly inhomogeneous and is sensitive to the physical properties of the cell and its environment. These findings provide insight into the mechanisms for frequency-dependent cell responses to EF that regulate cell function, which may have important implications for EF-based therapies and biotechnology development.
An integrative method for testing form–function linkages and reconstructed evolutionary pathways of masticatory specialization
Authors: Tseng Z. Jack , Flynn John J.
Published: May 2015

Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form–function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways.
Super-resolution in high-contrast media
Authors: Ammari Habib , Zhang Hai
Published: May 2015

A mathematical theory is developed to explain the super-resolution and super-focusing in high-contrast media. The approach is based on the resonance expansion of the Green function associated with the medium. It is shown that the super-resolution is due to sub-wavelength resonant modes excited in the medium which can propagate into the far-field.
Environmental fluctuations restrict eco-evolutionary dynamics in predator–prey system
Authors: Hiltunen Teppo , Ayan Gökçe B. , Becks Lutz
Published: May 2015

Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria–ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.
Infection of male rats withToxoplasma gondiiresults in enhanced delay aversion and neural changes in the nucleus accumbens core
Authors: Tan Donna , Soh Linda Jing Ting , Lim Lee Wei , Daniel Tan Chia Wei , Zhang Xiaodong , Vyas Ajai
Published: May 2015

Rats infected with the protozoan parasiteToxoplasma gondiiexhibit reduced avoidance of predator odours. This behavioural change is likely to increase transmission of the parasite from rats to cats. Here, we show that infection withT. gondiiincreases the propensity of the infected rats to make more impulsive choices, manifested as delay aversion in an intertemporal choice task. Concomitantly,T. gondiiinfection causes reduction in dopamine content and neuronal spine density of the nucleus accumbens core, but not of the nucleus accumbens shell. These results are consistent with a role of the nucleus accumbens dopaminergic system in mediation of choice impulsivity and goal-directed behaviours. Our observations suggest thatT. gondiiinfection in rats causes a syndromic shift in related behavioural constructs of innate aversion and making foraging decisions.
Context-dependent ‘safekeeping’ of foraging tools in New Caledonian crows
Authors: Klump Barbara C. , van der Wal Jessica E. M. , St Clair James J. H. , Rutz Christian
Published: May 2015

Several animal species use tools for foraging, such as sticks to extract embedded arthropods and honey, or stones to crack open nuts and eggs. While providing access to nutritious foods, these behaviours may incur significant costs, such as the time and energy spent searching for, manufacturing and transporting tools. These costs can be reduced by re-using tools, keeping them safe when not needed. We experimentally investigated what New Caledonian crows do with their tools between successive prey extractions, and whether they express tool ‘safekeeping’ behaviours more often when the costs (foraging at height), or likelihood (handling of demanding prey), of tool loss are high. Birds generally took care of their tools (84% of 176 prey extractions, nine subjects), either trapping them underfoot (74%) or storing them in holes (26%)—behaviours we also observed in the wild (19 cases, four subjects). Moreover, tool-handling behaviour was context-dependent, with subjects: keeping their tools safe significantly more often when foraging at height; and storing tools significantly more often in holes when extracting more demanding prey (under these conditions, foot-trapping proved challenging). In arboreal environments, safekeeping can prevent costly tool losses, removing a potentially important constraint on the evolution of habitual and complex tool behaviour.
Climate mediates the effects of disturbance on ant assemblage structure
Authors: Gibb Heloise , Sanders Nathan J. , Dunn Robert R. , Watson Simon , Photakis Manoli , Abril Silvia , Andersen Alan N. , Angulo Elena , Armbrecht Inge , Arnan Xavier , Baccaro Fabricio B. , Bishop Tom R. , Boulay Raphael , Castracani Cristina , Del Toro Israel , Delsinne Thibaut , Diaz Mireia , Donoso David A. , Enríquez Martha L. , Fayle Tom M. , Feener Donald H. , Fitzpatrick Matthew C. , Gómez Crisanto , Grasso Donato A. , Groc Sarah , Heterick Brian , Hoffmann Benjamin D. , Lach Lori , Lattke John , Leponce Maurice , Lessard Jean-Philippe , Longino John , Lucky Andrea , Majer Jonathan , Menke Sean B. , Mezger Dirk , Mori Alessandra , Munyai Thinandavha C. , Paknia Omid , Pearce-Duvet Jessica , Pfeiffer Martin , Philpott Stacy M. , de Souza Jorge L. P. , Tista Melanie , Vasconcelos Heraldo L. , Vonshak Merav , Parr Catherine L.
Published: May 2015

Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction among temperature, precipitation and disturbance shaped species richness and evenness. The effect was manifested through a failure of species richness to increase substantially with temperature in transformed habitats at low precipitation. At low precipitation levels, evenness increased with temperature in undisturbed sites, peaked at medium temperatures in disturbed sites and remained low in transformed sites. In warmer climates with lower rainfall, the effects of increasing disturbance on species richness and evenness were akin to decreases in temperature of up to 9°C. Anthropogenic disturbance and ongoing climate change may interact in complicated ways to shape the structure of assemblages, with hot, arid environments likely to be at greatest risk.
Three spectrally distinct photoreceptors in diurnal and nocturnal Australian ants
Authors: Ogawa Yuri , Falkowski Marcin , Narendra Ajay , Zeil Jochen , Hemmi Jan M.
Published: May 2015

Ants are thought to be special among Hymenopterans in having only dichromatic colour vision based on two spectrally distinct photoreceptors. Many ants are highly visual animals, however, and use vision extensively for navigation. We show here that two congeneric day- and night-active Australian ants have three spectrally distinct photoreceptor types, potentially supporting trichromatic colour vision. Electroretinogram recordings show the presence of three spectral sensitivities with peaks (λmax) at 370, 450 and 550 nm in the night-activeMyrmecia vindexand peaks at 370, 470 and 510 nm in the day-activeMyrmecia croslandi. Intracellular electrophysiology on individual photoreceptors confirmed that the night-activeM. vindexhas three spectral sensitivities with peaks (λmax) at 370, 430 and 550 nm. A large number of the intracellular recordings in the night-activeM. vindexshow unusually broad-band spectral sensitivities, suggesting that photoreceptors may be coupled. Spectral measurements at different temporal frequencies revealed that the ultraviolet receptors are comparatively slow. We discuss the adaptive significance and the probability of trichromacy inMyrmeciaants in the context of dim light vision and visual navigation.
Social learning and the replication process: an experimental investigation
Authors: Derex Maxime , Feron Romain , Godelle Bernard , Raymond Michel
Published: May 2015

Human cultural traits typically result from a gradual process that has been described as analogous to biological evolution. This observation has led pioneering scholars to draw inspiration from population genetics to develop a rigorous and successful theoretical framework of cultural evolution. Social learning, the mechanism allowing information to be transmitted between individuals, has thus been described as a simple replication mechanism. Although useful, the extent to which this idealization appropriately describes the actual social learning events has not been carefully assessed. Here, we used a specifically developed computer task to evaluate (i) the extent to which social learning leads to the replication of an observed behaviour and (ii) the consequences it has for fitness landscape exploration. Our results show that social learning does not lead to a dichotomous choice between disregarding and replicating social information. Rather, it appeared that individuals combine and transform information coming from multiple sources to produce new solutions. As a consequence, landscape exploration was promoted by the use of social information. These results invite us to rethink the way social learning is commonly modelled and could question the validity of predictions coming from models considering this process as replicative.
Prolixibacter denitrificans sp. nov., an iron-corroding, facultatively aerobic, nitrate-reducing bacterium isolated from crude oil, and emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans
Authors: Iino Takao , Sakamoto Mitsuo , Ohkuma Moriya
Published: May 2015

The facultatively aerobic, non-hydrogenotrophic, iron (Fe0)-corroding, nitrate-reducing Prolixibacter sp. strain MIC1-1T was characterized for representation of a novel species of the genus Prolixibacter. Strain MIC1-1T grew optimally at 35–37 °C, at pH 6.5 and with 2  % (w/v) NaCl. Strain MIC1-1T also grew fermentatively on some pentoses, hexoses, disaccharides and soluble starch. Succinic acid was the major end-product from d-glucose fermentation. Strain MIC1-1T was differentiated from the type strain of Prolixibacter bellariivorans by cell size, optimum growth temperature, range of temperature and NaCl for growth, and nitrate reduction. On the basis of phenotypic features and the phylogenetic position, a novel species of the genus Prolixibacter is proposed for strain MIC1-1T, to be named Prolixibacter denitrificans sp. nov. The type strain is MIC1-1T ( = JCM 18694T = NBRC 102688T = DSM 27267T). Emended descriptions of the genus Prolixibacter and Prolixibacter bellariivorans are also provided.
Structure of human dual-specificity phosphatase 7, a potential cancer drug target
Authors: Lountos George T. , Austin Brian P. , Tropea Joseph E. , Waugh David S.
Published: May 2015

Human dual-specificity phosphatase 7 (DUSP7/Pyst2) is a 320-residue protein that belongs to the mitogen-activated protein kinase phosphatase (MKP) subfamily of dual-specificity phosphatases. Although its precise biological function is still not fully understood, previous reports have demonstrated that DUSP7 is overexpressed in myeloid leukemia and other malignancies. Therefore, there is interest in developing DUSP7 inhibitors as potential therapeutic agents, especially for cancer. Here, the purification, crystallization and structure determination of the catalytic domain of DUSP7 (Ser141–Ser289/C232S) at 1.67 Å resolution are reported. The structure described here provides a starting point for structure-assisted inhibitor-design efforts and adds to the growing knowledge base of three-dimensional structures of the dual-specificity phosphatase family.
Cloning, expression, purification, crystallization and X-ray crystallographic analysis of CofB, the minor pilin subunit of CFA/III from human enterotoxigenicEscherichia coli
Authors: Kawahara Kazuki , Oki Hiroya , Fukakusa Shunsuke , Maruno Takahiro , Kobayashi Yuji , Motooka Daisuke , Taniguchi Tooru , Honda Takeshi , Iida Tetsuya , Nakamura Shota , Ohkubo Tadayasu
Published: May 2015

Colonization factor antigen III (CFA/III) is one of the virulence factors of human enterotoxigenicEscherichia coli(ETEC) that forms the long, thin, proteinaceous fibres of type IV pili through assembly of its major and minor subunits CofA and CofB, respectively. The crystal structure of CofA has recently been reported; however, the lack of structural information for CofB, the largest among the known type IV pilin subunits, hampers a comprehensive understanding of CFA/III pili. In this study, constructs of wild-type CofB with an N-terminal truncation and the corresponding SeMet derivative were cloned, expressed, purified and crystallized. The crystals belonged to the rhombohedral space groupR32, with unit-cell parametersa=b= 103.97,c= 364.57 Å for the wild-type construct anda=b= 103.47,c= 362.08 Å for the SeMet-derivatized form. Although the diffraction quality of these crystals was initially very poor, dehydration of the crystals substantially improved the resolution limit from ∼4.0 to ∼2.0 Å. The initial phase was solved by the single-wavelength anomalous dispersion (SAD) method using a dehydrated SeMet CofB crystal, which resulted in an interpretable electron-density map.
Expression, purification and crystallization of a family 55 β-1,3-glucanase fromChaetomium thermophilum
Authors: Papageorgiou Anastassios C. , Li Duochuan
Published: May 2015

A β-1,3-glucanase from the thermophilic fungusChaetomium thermophilumwas overexpressed inPichia pastoris, purified and crystallized in the presence of 1.8 Msodium/potassium phosphate pH 6.8 as a precipitant. Data to 2.0 Å resolution were collected in-house at 293 K from a single crystal. The crystal was found to belong to space groupP21, with unit-cell parametersa= 64.1,b= 85.8,c= 68.5 Å, β = 93.1° and one molecule in the asymmetric unit.
High-resolution crystal structure of the leucine-rich repeat domain of the human tumour suppressor PP32A (ANP32A)
Authors: Zamora-Caballero Sara , Šiaučiunaite-Gaubard Lina , Bravo Jeronimo
Published: May 2015

Acidic leucine-rich nuclear phosphoprotein 32A (PP32A) is a tumour suppressor whose expression is altered in many cancers. It is an apoptotic enhancer that stimulates apoptosome-mediated caspase activation and also forms part of a complex involved in caspase-independent apoptosis (the SET complex). Crystals of a fragment of human PP32A corresponding to the leucine-rich repeat domain, a widespread motif suitable for protein–protein interactions, have been obtained. The structure has been refined to 1.56 Å resolution. This domain was previously solved at 2.4 and 2.69 Å resolution (PDB entries 2je0 and 2je1, respectively). The new high-resolution structure shows some differences from previous models: there is a small displacement in the turn connecting the first α-helix (α1) to the first β-strand (β1), which slightly changes the position of α1 in the structure. The shift in the turn is observed in the context of a new crystal packing unrelated to those of previous structures.
The structure of a contact-dependent growth-inhibition (CDI) immunity protein fromNeisseria meningitidisMC58
Authors: Tan Kemin , Johnson Parker M. , Stols Lucy , Boubion Bryan , Eschenfeldt William , Babnigg Gyorgy , Hayes Christopher S. , Joachimiak Andrezj , Goulding Celia W.
Published: May 2015

Contact-dependent growth inhibition (CDI) is an important mechanism of intercellular competition between neighboring Gram-negative bacteria. CDI systems encode large surface-exposed CdiA effector proteins that carry a variety of C-terminal toxin domains (CdiA-CTs). All CDI+bacteria also produce CdiI immunity proteins that specifically bind to the cognate CdiA-CT and neutralize its toxin activity to prevent auto-inhibition. Here, the X-ray crystal structure of a CdiI immunity protein fromNeisseria meningitidisMC58 is presented at 1.45 Å resolution. The CdiI protein has structural homology to the Whirly family of RNA-binding proteins, but appears to lack the characteristic nucleic acid-binding motif of this family. Sequence homology suggests that the cognate CdiA-CT is related to the eukaryotic EndoU family of RNA-processing enzymes. A homology model is presented of the CdiA-CT based on the structure of the XendoU nuclease fromXenopus laevis. Molecular-docking simulations predict that the CdiA-CT toxin active site is occluded upon binding to the CdiI immunity protein. Together, these observations suggest that the immunity protein neutralizes toxin activity by preventing access to RNA substrates.
Functional characterization of heat-shock protein 90 fromOryza sativaand crystal structure of its N-terminal domain
Authors: Raman Swetha , Suguna Kaza
Published: May 2015

Heat-shock protein 90 (Hsp90) is an ATP-dependent molecular chaperone that is essential for the normal functioning of eukaryotic cells. It plays crucial roles in cell signalling, cell-cycle control and in maintaining proteome integrity and protein homeostasis. In plants, Hsp90s are required for normal plant growth and development. Hsp90s are observed to be upregulated in response to various abiotic and biotic stresses and are also involved in immune responses in plants. Although there are several studies elucidating the physiological role of Hsp90s in plants, their molecular mechanism of action is still unclear. In this study, biochemical characterization of an Hsp90 protein from rice (Oryza sativa; OsHsp90) has been performed and the crystal structure of its N-terminal domain (OsHsp90-NTD) was determined. The binding of OsHsp90 to its substrate ATP and the inhibitor 17-AAG was studied by fluorescence spectroscopy. The protein also exhibited a weak ATPase activity. The crystal structure of OsHsp90-NTD was solved in complex with the nonhydrolyzable ATP analogue AMPPCP at 3.1 Å resolution. The domain was crystallized by cross-seeding with crystals of the N-terminal domain of Hsp90 fromDictyostelium discoideum, which shares 70% sequence identity with OsHsp90-NTD. This is the second reported structure of a domain of Hsp90 from a plant source.
Structure ofChlamydomonas reinhardtiiTHB1, a group 1 truncated hemoglobin with a rare histidine–lysine heme ligation
Authors: Rice Selena L. , Boucher Lauren E. , Schlessman Jamie L. , Preimesberger Matthew R. , Bosch Jürgen , Lecomte Juliette T. J.
Published: May 2015

THB1 is one of several group 1 truncated hemoglobins (TrHb1s) encoded in the genome of the unicellular green algaChlamydomonas reinhardtii. THB1 expression is under the control of NIT2, the master regulator of nitrate assimilation, which also controls the expression of the only nitrate reductase in the cell, NIT1.In vitroand physiological evidence suggests that THB1 converts the nitric oxide generated by NIT1 into nitrate. To aid in the elucidation of the function and mechanism of THB1, the structure of the protein was solved in the ferric state. THB1 resembles other TrHb1s, but also exhibits distinct features associated with the coordination of the heme iron by a histidine (proximal) and a lysine (distal). The new structure illustrates the versatility of the TrHb1 fold, suggests factors that stabilize the axial ligation of a lysine, and highlights the difficulty of predicting the identity of the distal ligand, if any, in this group of proteins.
Self and world in lay interpretations of climate change
Authors: Denniss Rebecca Joy , Davison Aidan
Published: May 2015

Purpose

– This paper aims to report on an in-depth qualitative study that focuses on the convergence of the interpretive activities of knowing, living in and valuing the world in lay reasoning about climate change. Although awareness is growing that lay people interact with scientific knowledge about climate change in complex ways, relatively little is known about this interaction. Much quantitative research on public attitudes to climate change does little to draw out the cognitive and experiential processes by which lay people arrive at understandings of climate change.

Design/methodology/approach

– Through narrative analysis of qualitative interviews, this paper examines lay rationalities of climate change as a process of not only knowing the world (epistemology), but of being oriented towards the world (ontology) and valuing the world (axiology).

Findings

– The findings emphasise the extent of individual variation in lay interpretations of climate change, and their internal complexity. Almost all participants display differences in reasoning about climate change when considering their personal lives as compared to the wider, public world. Distinct accounts of self and world in lay rationalities are evident in the ways that participants imagine the future and express their feelings of culpability for and responsibility to act on climate change.

Originality/value

– This paper argues that lay reasoning about climate science does not just engage ways of knowing the world but also ways of being in and valuing the world so as to open up multiple trajectories for comprehension.
Climate change and military planning
Authors: Brzoska Michael
Published: May 2015

Purpose

– The paper aims to investigate the consequences of climate change for the future of armed forces and their presentation in national security documents.

Design/methodology/approach

– A classification of potential future military roles and functions is derived from relevant literature, resulting in six “military futures”. Frames are developed for these whose occurrence is counted in 53 authoritative documents on security policy and defense planning from 38 countries. Results are presented in descriptive statistics.

Findings

– The paper demonstrates that climate change has become an important issue for military planning. However, the directions in which it takes thinking about the future of armed forces differ widely. Among the six “military futures” identified, those linked to the function of disaster relief are most frequently found. However, the expansion of traditional military roles is also promoted. Rarer are suggestions for armed forces to became “greener” or “leaner”. In general, climate change provides an additional justification for continuing established paths for military planning.

Originality/value

– The paper makes two contributions to the existing literature. First, it provides a classification of potential future consequences of climate change for armed forces. Second, it empirically establishes, for a set of authoritative documents, the relative importance of differing expectation of the effects of climate change on the structure and functions of militaries.
Sharing the burden of financing the green climate fund in the Post-Kyoto era
Authors: Cui Lianbiao , Gui Huangbao
Published: May 2015

Purpose

– The purpose of this paper is to design several methods for enforcing developed countries’ responsibilities under the Green Climate Fund (GCF). The GCF has been one of the core subjects of the world climate summits held under the United Nations Framework Convention on Climate Change. However, the development of the GCF has not progressed smoothly, and many concerns remain unresolved.

Design/methodology/approach

– This paper illustrates three approaches for financing the GCF that vary in terms of the relative weights accorded to environmental responsibility and economic capacity. These three methods include the historical responsibility (HR) principle, the ability to pay (AP) principle and the preference score compromises (PSC) approach (which is a combination of the HR and the AP principles).

Findings

– The empirical analysis demonstrates that the USA is the largest contributor to the GCF under the HR principle due to the volume of its historical emissions, whereas the European Union bears the greatest financial responsibility under the AP principle, based on its gross domestic product. Under the PSC approach, the European Union and the USA each undertakes a financial burden that approximates 40 per cent of the total financing for the GCF. These nations are followed by Japan, which has a share of almost 9 per cent.

Originality/value

– This study is the first attempt to introduce the PSC concept into discussions regarding GCF financing. A scheme of burden sharing that combines environmental responsibility and economic capacity factors is developed and introduced. The respective weights assigned to the two factors are determined based on the Borda rule in voting theory, which avoids the arbitrary allocation of weights between the HR and the AP. These findings will be useful for mobilising the GCF in the Post-Kyoto era.
The impact on educational technology of a fatal airline accident: a case study
Authors: Brady Tim
Published: May 2015

Purpose

– The purpose of this paper is to study of how a virtual technology burden was created that impacted the professional pilot college student and various colleges/universities that offer professional pilot degree programs. A cascading set of events began as a result of US congressional reaction to a tragic airline accident. The resulting legislation forced the Federal Aviation Administration to publish new rules for first officer qualifications that were unmindful of the recommendations of professional pilot groups for simulation-based training. Ultimately, this placed a financial burden on both the college/university training curriculum and on the professional pilot student.

Design/methodology/approach

– This paper adopts a case study approach.

Findings

– Because of US congressional over-reaction, a collegiate system which produced excellent first officer candidates who had below 500 flight hours and who had been demonstrated scientifically to be efficient, skilled, and safe, was upended. The flight hour requirements were increased fivefold with little regard to its impact on the pilot pool. Congressional legislation forced the FAA to create and publish new rules that were unmindful of the simulation recommendations of professional pilot groups and required virtual simulation technology new to the college/university training environment.

Originality/value

– Traces the effect of government interference into a previously stable continuum of college-prepared airline pilots who are safe and effective.
Designing the online oral language learning environment SpeakApps
Authors: Nic Giolla Mhichíl Mairéad , Appel Christine , Ó Ciardubháin Colm , Jager Sake , Prizel-Kania Adriana
Published: May 2015

Purpose

– The purpose of this paper is to report on SpeakApps, a major collaborative computer-assisted language learning project, developed based on an open source techno-pedagogical solution to facilitate online oral language production and interaction.

Design/methodology/approach

– A mixed method approach was incorporated as part of the development process which included a comprehensive literature and practice review, user requirement survey of 815 learner, 61 pilot studies with 7,180 students, construction of qualitative teaching scenarios and a Delphi analysis.

Findings

– Language learners have limited experience of using synchronous communication tools within language learning contexts. Improving usability features within the Open Educational Resources supported the notion of sustainability and that the provision of the mechanism to indicate quality were vital to support the integrity of open content.

Originality/value

– The paper provides an overview of the operationalisation of an action-oriented approach to language learning which manifested as a design for learning development process. It illustrates the breadth of issues raised from technical to pedagogical when teacher and learner agency are central for development and sustainability.
Cooperative purchase and use: a study of the ProQuest full text database of dissertations and theses (PQDT)
Authors: Yao Xiaoxia , Zhao YongChao
Published: May 2015

Purpose

– To purpose of this study is to describe and to demonstrate the value of a consortium purchase of the ProQuest Dissertations and Theses full-text database (PQDT) in China.

Design/methodology/approach

– The authors provide a first-person account based on their professional positions at the China Academic Library & Information System Administrative Center.

Findings

– That the PQDT database has steadily increased the use of theses in China with more institutions subscribing every year. The PQDT full-text database has become one of the most cost effective databases cooperatively purchased in China.

Originality/value

– One of the few in-depth studies of the use of the PQDT database.
Open Doors: library cross-sector co-operation in Bristol, UK
Authors: Chelin Jacqueline Ann
Published: May 2015

Purpose

– This paper outlines the aims, activities and outcomes of a project to pilot a reciprocal borrowing scheme between public and academic libraries using existing cards, i.e. public library cards in the academic library and university ID cards in the public libraries.

Design/methodology/approach

– This is a case study providing practical information about the establishment and promotion of the service, and recounting the feedback from surveys of participants, prospective users and library staff.

Findings

– The project outcomes indicate that the reciprocal use of existing library cards between institutions and public libraries in a geographical area: was relatively simple once set up; was appreciated by all those who participated; had few teething problems; had had no appreciable impact on the availability of academic stock to University of the West of England (UWE) students; increased public library and academic library usage by target groups, e.g. school students 16 years and over, enabled the public library service to provide a significantly better offer of resources to its community, especially those who needed access to specialised stock, not normally available in a general public library service.

Originality/value

– The partnership between LibrariesWest (led by South Gloucestershire Libraries) and UWE Bristol Library Services is not unusual. However, the approach taken, i.e. to allow borrowers to use their own libraries’ cards without any data sharing between the respective systems, is fairly unique. The processes involved and the evaluation of the scheme are of value to other prospective partnerships where organisations are geographically aligned.
When small businesses go international: alliances as a key to entry
Authors: Haase Heiko , Franco Mário
Published: May 2015

Purpose

– The purpose of this study is to identify the reasons for the internationalisation of small and medium-sized enterprises (SMEs) through strategic alliances and to understand how this internationalisation process evolves.

Design/methodology/approach

– For this purpose, the authors decided on a qualitative approach and performed exploratory case studies of two SMEs in Portugal.

Findings

– The authors found that in forming alliances, SMEs aim to increase sales and reduce costs. After the analysis, the authors believe that learning about other markets and cultures as well as having appropriate national partners are the key aspects in the internationalisation of SMEs through strategic alliances.

Practical implications

– The authors revealed the influence of national partners in the internationalisation process. The firms in the study established alliances with national firms to facilitate international market entry. This holds in particular for partners that already have some international experience. Building partnerships with national firms allows the combination of competencies and requires a lower amount of internationalisation know-how on the part of the cooperating firms.

Originality/value

– In spite of the opportunities going along with strategic alliances, there is only limited empirical evidence of their impact on the internationalisation process and vice-versa. This holds particularly true for the realm of SMEs.