bluuebunny/crossref_metadata_2025 huggingface dataset:
Agroinfiltration by Cytokinin-Producing Agrobacterium sp. Strain GV3101 Primes Defense Responses in Nicotiana tabacum
Authors: Sheikh Arsheed Hussain , Raghuram Badmi , Eschen-Lippold Lennart , Scheel Dierk , Lee Justin , Sinha Alok Krishna
Published: July 2014

Transient infiltrations in tobacco are commonly used in plant studies, but the host response to different disarmed Agrobacterium strains is not fully understood. The present study shows that pretreatment with disarmed Agrobacterium tumefaciens GV3101 primes the defense response to subsequent infection by Pseudomonas syringae in Nicotiana tabacum. The presence of a trans-zeatin synthase (tzs) gene in strain GV3101 may be partly responsible for the priming response, as the tzs-deficient Agrobacterium sp. strain LBA4404 only weakly imparts such responses. Besides inducing the expression of defense-related genes like PR-1 and NHL10, GV3101 pretreatment increased the expression of tobacco mitogen-activated protein kinase (MAPK) pathway genes like MEK2, WIPK (wound-induced protein kinase), and SIPK (salicylic acid-induced protein kinase). Furthermore, the GV3101 strain showed a stronger effect than the LBA4404 strain in activating phosphorylation of the tobacco MAPK, WIPK and SIPK, which presumably prime the plant immune machinery. Lower doses of exogenously applied cytokinins increased the activation of MAPK, while higher doses decreased the activation, suggesting a balanced level of cytokinins is required to generate defense response in planta. The current study serves as a cautionary warning for plant researchers over the choice of Agrobacterium strains and their possible consequences on subsequent pathogen-related studies.
Citrus Viroids: Symptom Expression and Performance of Washington Navel Sweet Orange Trees Grafted on Carrizo Citrange
Authors: Murcia N. , Hashemian S. M. Bani , Serra P. , Pina J. A. , Duran-Vila N.
Published: July 2014

Citrus are natural hosts of several viroid species. Citrus exocortis viroid (CEVd) and Hop stunt viroid (HSVd) are the causal agents of two well-known diseases of citrus, exocortis and cachexia. Other viroids have been found to induce specific symptoms and different degrees of stunting in trees grafted on trifoliate orange and trifoliate orange hybrids. A field assay was initiated in 1989 to establish the effect of CEVd, HSVd, Citrus bent leaf viroid (CBLVd), Citrus dwarfing viroid (CDVd), and Citrus bark cracking viroid (CBCVd) on Washington navel sweet orange trees grafted on Carrizo citrange rootstock. Here we report the effect of viroid infection on symptom expression, tree size, fruit production and quality evaluated from 2004 to 2007. Vegetative growth was affected by viroid infection with height and canopy volume being reduced. No bark scaling symptoms were observed in CEVd-infected trees albeit they presented lesions and blisters in the roots. Bark cracking symptoms were consistently observed in CBCVd-infected trees that were smaller with enhanced productivity and fruit size. No major effects were found as a result of infection with CBLVd, HSVd, or CDVd. The quality of the fruits was not affected by viroid infection, except for the low diameter of the fruits harvested from HSVd-infected trees. An interesting effect was identified in terms of tree productivity increase (yield/canopy volume) as a result of infection with CEVd, CDVd, and especially CBCVd.
First Report of a Leaf Spot of Radermachera sinica in China Caused by Bacillus megaterium
Authors: Li Y. L. , Zhou Z. , Yuan Y. C. , Ye J. R.
Published: July 2014

Radermachera sinica is widely planted as an ornamental plant in homes, offices, and malls in China. A leaf spot of R. sinica occurred in Luoyang, China, from 2013 to 2014. Lesions mostly occurred in wounds and were irregular with light brown centers and purple borders. One or more lesions on a leaf sometimes covered the entire blade. Eighty plants were surveyed in Luoyang, with disease incidence of 17%. Five millimeter pieces from the borders of lesions were surface-disinfected with 75% ethanol for 30 s, 1% sodium hypochlorite for 5 min, washed three times in sterilized distilled water, placed on nutrient agar (NA) medium at 25°C in darkness, and incubated for 24 to 48 h. Four white, round, smooth, and shiny colonies were selected for further identification. All strains were gram-positive, aerobic rods with many peritrichous flagella, and could grow in medium containing 5% NaCl. The strains were positive for catalase, starch hydrolysis, liquefaction of gelatin, reduction of nitrate, acid production from glucose, mannitol, maltose, lactose, xylose, and pectinose. The strains were positive for phenylalanine deaminase, decomposition of tyrosine, and utilization of citrate. The strains were identified by biochemical tests as Bacillus megaterium (1). To confirm pathogenicity, the strains were grown on NA for 48 h and suspended in sterile distilled water to produce a suspension with a final concentration of 108 CFU/ml. Healthy leaves of biennial R. sinica plants were sterilized with 75% ethanol and washed three times with sterilized distilled water. Fresh wounds were made with a sterile needle on the healthy leaves. Each of four strains was tested by spray inoculation with a bacterial suspension on three leaves. Sterile distilled water was used as negative control. Plants were enclosed in plastic bags and placed in a growth chamber at 28°C with 80% relative humidity. After 5 days, water-soaked lesions were observed. Two weeks later, lesions 4 mm in diameter turned light brown with purple borders, and most of lesions occurred in puncture wounds. Symptoms similar to those observed on field plants developed on all inoculated leaves, while no symptoms appeared on the control leaves. B. megaterium was re-isolated from the lesions of inoculated leaves, but not from the control leaves. To confirm the bacterial identification, PCR was performed on the 16S rDNA gene with P1/P2 (P1: CAGAGTTTGATCCTGGCT, P2: AGGAGGTGATCCAGCCGCA) (2) and 1,463 bp of the 16S rDNA gene (GenBank Accession No. KJ789369) showed 100% sequence identity to B. megaterium DSM 319 (NC_014103.1). To our knowledge, this is the first report of a leaf spot of R. sinica caused by B. megaterium in China as well as anywhere in the world.

References: (1) P. Vos et al. Bergey's Manual of Systematic Bacteriology. Vol 3: The Firmicutes. Springer, 2009. (2) W. G. Weisbury et al. J. Bacteriol. 173:697, 1991.
Selected Pacific Northwest Rangeland and Weed Plants as Hosts of Pratylenchus neglectus and P. thornei
Authors: Smiley Richard W. , Yan Guiping , Gourlie Jennifer A.
Published: July 2014

Eighteen rangeland plants and 16 weed species were assayed in the greenhouse for efficiency as hosts of Pratylenchus neglectus and P. thornei. Hosting ability ratings were assigned using the ratio of final versus initial nematode density and by comparing the final nematode density to that of susceptible wheat controls. Good hosts of both Pratylenchus spp. included thickspike bluegrass ‘Critana’, smooth brome ‘Manchar’, seven wheatgrasses, and jointed goatgrass. Good hosts of P. neglectus but not P. thornei included two hairy vetches, western wheatgrass ‘Rosana’, big bluegrass ‘Sherman’, tall wheatgrass ‘Alkar’, green foxtail, kochia, large crabgrass, palmer amaranth, redroot pigweed, tumble mustard, and wild oat. Good hosts of P. thornei but not P. neglectus included hard fescue ‘Durar’, sheep fescue ‘Blacksheep’, downy brome, and rattail fescue. Poor or minor hosts of both Pratylenchus spp. included two alfalfas, dandelion, horseweed, lambsquarters, prostrate spurge, and Russian thistle. These assays will provide guidance for transitioning rangeland into crop production and for understanding the role of weeds on densities of Pratylenchus spp. in wheat-production systems.
The structure and mechanics of Moso bamboo material
Authors: Dixon P. G. , Gibson L. J.
Published: July 2014

Although bamboo has been used structurally for millennia, there is currently increasing interest in the development of renewable and sustainable structural bamboo products (SBPs). These SBPs are analogous to wood products such as plywood, oriented strand board and glue-laminated wood. In this study, the properties of natural Moso bamboo (
Phyllostachys pubescens
) are investigated to further enable the processing and design of SBPs. The radial and longitudinal density gradients in bamboo give rise to variations in the mechanical properties. Here, we measure the flexural properties of Moso bamboo in the axial direction, along with the compressive strengths in the axial and transverse directions. Based on the microstructural variations (observed with scanning electron microscopy) and extrapolated solid cell wall properties of bamboo, we develop models, which describe the experimental results well. Compared to common North American construction woods loaded along the axial direction, Moso bamboo is approximately as stiff and substantially stronger, in both flexure and compression but denser. This work contributes to critical knowledge surrounding the microstructure and mechanical properties of bamboo, which are vital to the engineering and design of sustainable SBPs.
Ultrasonic emissions reveal individual cavitation bubbles in water-stressed wood
Authors: Ponomarenko A. , Vincent O. , Pietriga A. , Cochard H. , Badel É. , Marmottant P.
Published: July 2014

Under drought conditions, the xylem of trees that conducts ascending sap produces ultrasonic emissions whose exact origin is not clear. We introduce a new method to record simultaneously both acoustic events and optical observation of the xylem conduits within slices of wood that were embedded in a transparent material setting a hydric stress. In this article, we resolved the rapid development of all cavitation bubbles and demonstrated that each ultrasound emission was linked to the nucleation of one single bubble, whose acoustic energy is an increasing function of the size of the conduit where nucleation occurred and also of the hydric stress. We modelled these observations by the fact that water columns in conduits store elastic energy and release it into acoustic waves when they are broken by cavitation bubbles. Water columns are thus elastic, and not rigid, ‘wires of water’ set under tension by hydric stresses. Cavitation bubbles are at the origin of an embolism, whose development was followed in our experiments. Such an embolism of sap circulation can result in a fatal condition for living trees. These findings provide new insights for the non-destructive monitoring of embolisms within trees, and suggest a new approach to study porous media under hydric stress.
To react or not to react? Intrinsic stochasticity of human control in virtual stick balancing
Authors: Zgonnikov Arkady , Lubashevsky Ihor , Kanemoto Shigeru , Miyazawa Toru , Suzuki Takashi
Published: July 2014

Understanding how humans control unstable systems is central to many research problems, with applications ranging from quiet standing to aircraft landing. Increasingly, much evidence appears in favour of event-driven control hypothesis: human operators only start actively controlling the system when the discrepancy between the current and desired system states becomes large enough. The event-driven models based on the concept of threshold can explain many features of the experimentally observed dynamics. However, much still remains unclear about the dynamics of human-controlled systems, which likely indicates that humans use more intricate control mechanisms. This paper argues that control activation in humans may be not threshold-driven, but instead intrinsically stochastic, noise-driven. Specifically, we suggest that control activation stems from stochastic interplay between the operator's need to keep the controlled system near the goal state, on the one hand, and the tendency to postpone interrupting the system dynamics, on the other hand. We propose a model capturing this interplay and show that it matches the experimental data on human balancing of virtual overdamped stick. Our results illuminate that the noise-driven activation mechanism plays a crucial role at least in the considered task, and, hypothetically, in a broad range of human-controlled processes.
Cones of localized shear strain in incompressible elasticity with prestress: Green's function and integral representations
Authors: Argani L. P. , Bigoni D. , Capuani D. , Movchan N. V.
Published: July 2014

The infinite-body three-dimensional Green's function set (for incremental displacement and mean stress) is derived for the incremental deformation of a uniformly strained incompressible, nonlinear elastic body. Particular cases of the developed formulation are the Mooney–Rivlin elasticity and the J
2
-deformation theory of plasticity. These Green's functions are used to develop a boundary integral equation framework, by introducing an
ad hoc
potential, which paves the way for a boundary element formulation of three-dimensional problems of incremental elasticity. Results are used to investigate the behaviour of a material deformed near the limit of ellipticity and to reveal patterns of shear failure. In fact, within the investigated three-dimensional framework, localized deformations emanating from a perturbation are shown to be organized in conical geometries rather than in planar bands, so that failure is predicted to develop through curved and thin surfaces of intense shearing, as can for instance be observed in the cup–cone rupture of ductile metal bars.
Is adaptation to climate change really constrained in niche specialists?
Authors: van Heerwaarden Belinda , Sgrò Carla M.
Published: July 2014

Species with restricted distributions make up the vast majority of biodiversity. Recent evidence suggests thatDrosophilaspecies with restricted tropical distributions lack genetic variation in the key trait of desiccation resistance. It has therefore been predicted that tropically restricted species will be limited in their evolutionary response to future climatic changes and will face higher risks of extinction. However, these assessments have been made using extreme levels of desiccation stress (less than 10% relative humidity (RH)) that extend well beyond the changes projected for the wet tropics under climate change scenarios over the next 30 years. Here, we show that significant evolutionary responses to less extreme (35% RH) but more ecologically realistic levels of climatic change and desiccation stress are in fact possible in two species of rainforest restrictedDrosophila. Evolution may indeed be an important means by which sensitive rainforest-restricted species are able to mitigate the effects of climate change.
Geobacter anodireducens sp. nov., an exoelectrogenic microbe in bioelectrochemical systems
Authors: Sun Dan , Wang Aijie , Cheng Shaoan , Yates Matthew , Logan Bruce E.
Published: July 2014

A previously isolated exoelectrogenic bacterium, strain SD-1T, was further characterized and identified as a representative of a novel species of the genus

Geobacter

. Strain SD-1T was Gram-negative, aerotolerant, anaerobic, non-spore-forming, non-fermentative and non-motile. Cells were short, curved rods (0.8–1.3 µm long and 0.3 µm in diameter). Growth of strain SD-1T was observed at 15–42 °C and pH 6.0–8.5, with optimal growth at 30–35 °C and pH 7. Analysis of 16S rRNA gene sequences indicated that the isolate was a member of the genus

Geobacter

, with the closest known relative being

Geobacter sulfurreducens

PCAT (98 % similarity). Similar to other members of the genus

Geobacter

, strain SD-1T used soluble or insoluble Fe(III) as the sole electron acceptor coupled with the oxidation of acetate. However, SD-1T could not reduce fumarate as an electron acceptor with acetate oxidization, which is an important physiological trait for

G. sulfurreducens

. Moreover, SD-1T could grow in media containing as much as 3 % NaCl, while

G. sulfurreducens

PCAT can tolerate just half this concentration, and this difference in salt tolerance was even more obvious when cultivated in bioelectrochemical systems. DNA–DNA hybridization analysis of strain SD-1T and its closest relative,

G. sulfurreducens

ATCC 51573T, showed a relatedness of 61.6 %. The DNA G+C content of strain SD-1T was 58.9 mol%. Thus, on the basis of these characteristics, strain SD-1T was not assigned to

G. sulfurreducens

, and was instead classified in the genus

Geobacter

as a representative of a novel species. The name Geobacter anodireducens sp. nov. is proposed, with the type strain SD-1T ( = CGMCC 1.12536T = KCTC 4672T).
Microbacterium hydrothermale sp. nov., an actinobacterium isolated from hydrothermal sediment
Authors: Zhang Yubian , Ren Huihui , Zhang Gaiyun
Published: July 2014

A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, strain 0704C9-2T, was isolated from hydrothermal sediment of the Indian Ocean. The organism grew with 0–5 % (w/v) NaCl and at 10–37 °C, with optimal growth occurring with 1 % NaCl and at 28–30 °C. Comparative 16S rRNA gene sequence analysis revealed that strain 0704C9-2T belonged to the genus

Microbacterium

. It exhibited highest 16S rRNA gene sequence similarity with

Microbacterium testaceum

DSM 20166T (98.4 %). Levels of similarity with the type strains of all other recognized species of the genus

Microbacterium

were less than 98.0 %. DNA–DNA hybridization experiments with strain 0704C9-2T and its closest relative,

M. testaceum

DSM 20166T, revealed a low reassociation value of 42.9 %. The DNA G+C content of strain 0704C9-2T was 73.3 mol%. The cell-wall peptidoglycan contained ornithine and the acyl type was glycolyl. The major whole-cell sugars were mannose, galactose, rhamnose and glucose. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The predominant menaquinones were MK-11, MK-10 and MK-12. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and an unknown phospholipid. On the basis of phenotypic, phylogenetic and genotypic data, strain 0704C9-2T represents a novel species within the genus

Microbacterium

, for which the name Microbacterium
hydrothermale sp. nov. is proposed. The type strain is 0704C9-2T ( = LMG 27542T = CGMCC 1.12512T).
Glycomyces artemisiae sp. nov., an endophytic actinomycete isolated from the roots of Artemisia argyi
Authors: Zhang Xiumin , Ren Kai , Du Jiao , Liu Haiyan , Zhang Liping
Published: July 2014

An endophytic actinomycete strain, IXS4T, was isolated from the root of Artemisia argyi, a medicinal plant collected from Yesanpo located in Laishui county, Hebei province, China. The 16S rRNA gene sequence of strain IXST showed most similarity to

Glycomyces mayteni

YIM 61331T (98.23 % 16S rRNA gene sequence similarity),

Glycomyces scopariae

YIM 56256T (98.00 %),

Glycomyces sambucus

E71T (97.90 %) and

Glycomyces algeriensis

NRRL B-16327T (97.10 %). DNA–DNA hybridization values between strain IXS4T and the closely related type strains were well below 70 %. The strain also showed a number of physiological and biochemical characteristics that were distinct from the closely related species. The strain contained MK-10(H2) and MK-11(H0) as the detected menaquinones. The peptidoglycan was mainly meso-diaminopimelic acid and the whole-cell sugars contained galactose, glucose, mannose, xylose and ribose. The major cellular fatty acids were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. Based on the genetic and phenotypic properties, it is proposed that strain IXS4T represents a novel species of the genus

Glycomyces

, with the name http://dx.doi.org/10.1601/nm.7671
Glycomyces artemisiae sp. nov. The type strain is IXS4T ( = HBUM178000T = CGMCC 4.7067T = NBRC 109773T).
Phaeodactylibacter xiamenensis gen. nov., sp. nov., a member of the family Saprospiraceae isolated from the marine alga Phaeodactylum tricornutum
Authors: Chen Zhangran , Lei Xueqian , Lai Qiliang , Li Yi , Zhang Bangzhou , Zhang Jingyan , Zhang Huajun , Yang Luxi , Zheng Wei , Tian Yun , Yu Zhiming , Xu Hong , Zheng Tianling
Published: July 2014

A novel Gram-staining-negative, aerobic, rod-shaped, non-motile, reddish-orange and chemoheterotrophic bacteria, designated strain KD52T, was isolated from a culture of the alga Phaeodactylum tricornutum from Xiamen, Fujian Province, China. 16S rRNA gene sequence comparison showed that strain KD52T was a member of the family

Saprospiraceae

, forming a distinct lineage with ‘Portibacter lacus’ KCTC 23747. The 16S rRNA gene sequence similarity between strain KD52T and the type strains of species of the family

Saprospiraceae

ranged from 86 % to 89 %. Growth occurred at 20–37 °C (optimum, 28 °C), in the presence of 1–9 % (w/v) NaCl (optimum, 2.5 %) and at pH 5–8.5 (optimum, pH 6.0). The dominant fatty acids (>10 %) of strain KD52T were iso-C15 : 0 (33.1 %), iso-C15 : 1 G (14.8 %) and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 13.8 %). The major polar lipids were diphosphatidylglycerol, three unidentified phospholipids, four unknown lipids and one unidentified aminolipid. The DNA G+C content was 51 mol% and the major respiratory quinone was menaquinone-7 (MK-7). On the basis of phenotypic data and phylogenetic inference, strain KD52T represents a novel species of a new genus, for which the name Phaeodactylibacter xiamenensis gen. nov., sp. nov., is proposed. The type strain is KD52T ( = MCCC 1F01213T = KCTC 32575T).
Permianibacter aggregans gen. nov., sp. nov., a bacterium of the family Pseudomonadaceae capable of aggregating potential biofuel-producing microalgae
Authors: Wang Hui , Zheng Tianling , Hill Russell T. , Hu Xiaoke
Published: July 2014

A novel bacterial strain, capable of aggregating potential biofuel-producing microalgae, was isolated from the phycosphere of an algal culture and designated HW001T. The novel bacterial strain was identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics in this study. Cells were aerobic, Gram-negative rods. 16S rRNA gene-based phylogenetic analysis revealed that strain HW001T is affiliated with the family

Pseudomonadaceae

in the phylum

Proteobacteria

, but forms a distinct clade within this family. The DNA G+C content of strain HW001T was 55.4 mol%. The predominant cellular fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c), C16 : 0 and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). Q-8 was the main respiratory quinone. The polar lipid profile contained phosphatidylethanolamine, an unidentified aminophospholipid and some unidentified lipids. Based on the extensive polyphasic analysis, strain HW001T represents a novel species of a new genus in the family

Pseudomonadaceae

, for which the name Permianibacter aggregans gen. nov., sp. nov., is proposed. The type strain of the type species is HW001T ( = CICC 10856T = KCTC 32485T).
Dormant bacteria within Staphylococcus epidermidis biofilms have low inflammatory properties and maintain tolerance to vancomycin and penicillin after entering planktonic growth
Authors: Cerca Filipe , França Ângela , Pérez-Cabezas Begoña , Carvalhais Virgínia , Ribeiro Adília , Azeredo Joana , Pier Gerald , Cerca Nuno , Vilanova Manuel
Published: July 2014

Staphylococcus epidermidis is the most commonly isolated aetiological agent of nosocomial infections, mainly due to its ability to establish biofilms on indwelling medical devices. Detachment of bacteria from S. epidermidis biofilms and subsequent growth in the planktonic form is a hallmark of the pathogenesis of these infections leading to dissemination. Here we showed that S. epidermidis cells collected from biofilms cultured in conditions that promote cell viability present marked changes in their physiological status upon initiating a planktonic mode of growth. When compared to cells growing in biofilms, they displayed an increased SYBR green I staining intensity, increased transcription of the rpiA gene, decreased transcription of the icaA gene, as well as higher susceptibility to vancomycin and penicillin. When bacteria collected from biofilms with high proportions of dormant cells were subsequently cultured in the planktonic mode, a large proportion of cells maintained a low SYBR green I staining intensity and increased resistance to vancomycin and penicillin, a profile typical of dormant cells. This phenotype further associated with a decreased ability of these biofilm-derived cells to induce the production of pro-inflammatory cytokines by bone marrow-derived dendritic cells in vitro. These results demonstrated that cells detached from the biofilm maintain a dormant cell-like phenotype, having a low pro-inflammatory effect and decreased susceptibility to antibiotics, suggesting these cells may contribute to the recalcitrant nature of biofilm infections.
Extreme expansion of the olfactory receptor gene repertoire in African elephants and evolutionary dynamics of orthologous gene groups in 13 placental mammals
Authors: Niimura Yoshihito , Matsui Atsushi , Touhara Kazushige
Published: July 2014

Olfactory receptors (ORs) detect odors in the environment, and OR genes constitute the largest multigene family in mammals. Numbers of OR genes vary greatly among species—reflecting the respective species' lifestyles—and this variation is caused by frequent gene gains and losses during evolution. However, whether the extent of gene gains/losses varies among individual gene lineages and what might generate such variation is unknown. To answer these questions, we used a newly developed phylogeny-based method to classify >10,000 intact OR genes from 13 placental mammal species into 781 orthologous gene groups (OGGs); we then compared the OGGs. Interestingly, African elephants had a surprisingly large repertoire (∼2000) of functional OR genes encoded in enlarged gene clusters. Additionally, OR gene lineages that experienced more gene duplication had weaker purifying selection, and Class II OR genes have evolved more dynamically than those in Class I. Some OGGs were highly expanded in a lineage-specific manner, while only three OGGs showed complete one-to-one orthology among the 13 species without any gene gains/losses. These three OGGs also exhibited highly conserved amino acid sequences; therefore, ORs in these OGGs may have physiologically important functions common to every placental mammal. This study provides a basis for inferring OR functions from evolutionary trajectory.
TAA1-Regulated Local Auxin Biosynthesis in the Root-Apex Transition Zone Mediates the Aluminum-Induced Inhibition of Root Growth inArabidopsis
Authors: Yang Zhong-Bao , Geng Xiaoyu , He Chunmei , Zhang Feng , Wang Rong , Horst Walter J. , Ding Zhaojun
Published: July 2014

The transition zone (TZ) of the root apex is the perception site of Al toxicity. Here, we show that exposure of Arabidopsis thaliana roots to Al induces a localized enhancement of auxin signaling in the root-apex TZ that is dependent on TAA1, which encodes a Trp aminotransferase and regulates auxin biosynthesis. TAA1 is specifically upregulated in the root-apex TZ in response to Al treatment, thus mediating local auxin biosynthesis and inhibition of root growth. The TAA1-regulated local auxin biosynthesis in the root-apex TZ in response to Al stress is dependent on ethylene, as revealed by manipulating ethylene homeostasis via the precursor of ethylene biosynthesis 1-aminocyclopropane-1-carboxylic acid, the inhibitor of ethylene biosynthesis aminoethoxyvinylglycine, or mutant analysis. In response to Al stress, ethylene signaling locally upregulates TAA1 expression and thus auxin responses in the TZ and results in auxin-regulated root growth inhibition through a number of auxin response factors (ARFs). In particular, ARF10 and ARF16 are important in the regulation of cell wall modification–related genes. Our study suggests a mechanism underlying how environmental cues affect root growth plasticity through influencing local auxin biosynthesis and signaling.
How detectable is predation in stage‐structured populations? Insights from a simulation‐testing analysis
Authors: Oken Kiva L. , Essington Timothy E.
Published: July 2014

The potential of predation to structure marine food webs is widely acknowledged. However, available tools to detect the regulation of prey population dynamics by predation are limited, partly because available population data often aggregate a population's age structure into a single biomass or abundance metric. Additionally, many food webs are relatively complex, with prey species subject to different assemblages of predators throughout their ontogeny.

The goal of this study was to evaluate the extent to which stage‐structured predation could be reliably detected from time series of total biomass of predators and prey.

We simulated age‐structured populations of four mid‐trophic‐level fish species with distinct life‐history traits, exposed them to variable predation at different life stages and fit production models to resulting population biomass to determine how reliably the effects of predators could be detected.

Predation targeting early life history and juvenile life stages generally led to larger fluctuations in annual production and was therefore more detectable. However, ecologically realistic levels of observation error and environmental stochasticity masked most predator signals. The addition of predation at a second life stage sharply decreased the ability to detect the effect of each predator.

We conclude that the absence of detectable species interactions from biomass time series may be partly due to the interactive effects of environmental variability and complex food web linkages and life histories. We also note that predation signals are most robust for predator–prey systems where predators primarily act on mortality of submature life‐history stages. Simulation testing can be applied widely to evaluate the statistical power of analyses to detect predation effects.
A host as an ecosystem:Wolbachiacoping with environmental constraints
Authors: Sicard Mathieu , Dittmer Jessica , Grève Pierre , Bouchon Didier , Braquart‐Varnier Christine
Published: July 2014

TheWolbachiaare intracellular endosymbionts widely distributed among invertebrates. These primarily vertically transmittedα‐proteobacteriahave been intensively studied during the last decades because of their intriguing interactions with hosts, ranging from reproductive manipulations to mutualism. To optimize their vertical transmission from mother to offspring, theWolbachiahave developed fine‐tuned strategies. However, theWolbachiaare not restricted to the female gonads and frequently exhibit wide intra‐host distributions. This extensive colonization of somatic organs might be necessary forWolbachiato develop their diverse extended phenotypes. From an endosymbiont's perspective, the within‐host environment potentially presents different environmental constraints. Hence, theWolbachiahave to face different intracellular habitats, their host's immune system as well as other microorganisms co‐occurring in the same host individual and sometimes even in the same cell. A means for theWolbachiato protect themselves from these environmental constraints may be to live ‘hidden’ in vacuoles within host cells. In this review, we summarize the current knowledge regarding the extent of theWolbachiapandemic and discuss the various environmental constraints these bacteria may have to face within their ‘host ecosystem’. Finally, we identify new avenues for future research to better understand the complexity ofWolbachia's interactions with their intracellular environment.
The inequality trap. A comparative analysis of social spending between 1880 and 1930
Authors: Espuelas Sergio
Published: July 2014

It is often assumed that the fight against inequality played an important role in the rise of the welfare state. However, using social transfers as an indicator of redistribution and three alternative proxies for inequality—the top income shares, the ratio of theGDPper capita to the unskilled wage, and the share of non‐family farms—this article shows that inequality did not favour the development of social policy between 1880 and 1930. On the contrary, social policy developed more easily in countries that were previously more egalitarian, suggesting that unequal societies were in a sort of inequality trap, where inequality itself was an obstacle to redistribution.
Formulation of apple juice beverages containing whey protein isolate or whey protein hydrolysate based on sensory and physicochemical analysis
Authors: Goudarzi Mostafa , Madadlou Ashkan , Mousavi Mohammad E , Emam‐Djomeh Zahra
Published: July 2014

Whey protein isolate (WPI) or its bioactive hydrolysate (WPH) was mixed with apple juice along with sweetener, obtaining a series of beverages with various pH values. Sedimentation of WPI‐apple juice and WPH‐apple juice beverages was inhibited at pH values of 3.15 and 3.47, respectively. The higher the whey protein content, the more undesirable was the taste of samples. A clearer appearance with smaller particle size was obtained with WPH‐apple juice formulations compared to WPI‐apple juice formulations at pH values closer to the pI of the whey proteins. Intrinsic viscosity measurements revealed the weaker associations of peptides compared with protein molecules.
The Prevalence of Encoded Digital Trace Evidence in the Nonfile Space of Computer Media,,
Authors: Garfinkel Simson L.
Published: July 2014

Forensically significant digital trace evidence that is frequently present in sectors of digital media not associated with allocated or deleted files. Modern digital forensic tools generally do not decompress such data unless a specific file with a recognized file type is first identified, potentially resulting in missed evidence. Email addresses are encoded differently for different file formats. As a result, trace evidence can be categorized as Plain in File (PF), Encoded in File (EF), Plain Not in File (PNF), or Encoded Not in File (ENF). The tool bulk_extractor finds all of these formats, but other forensic tools do not. A study of 961 storage devices purchased on the secondary market and shows that 474 contained encoded email addresses that were not in files (ENF). Different encoding formats are the result of different application programs that processed different kinds of digital trace evidence. Specific encoding formats explored include BASE64, GZIP, PDF, HIBER, and ZIP.
Bushfires, Human Health Economics, and Pyrogeography
Authors: BOWMAN DAVID , JOHNSTON FAY
Published: July 2014

Bushfires (landscape fires) are a key Earth system process that affects humans and our societies and economies. In a recent article, we explored the coupling of humans to landscape fire through the lens of human health impacts of bushfire smoke. We noted that such an approach demands recognition of the indirect impacts and costs of bushfires that cannot be captured by simplistic proxies such as deaths directly attributable to a fire front. Evaluation of direct and indirect economic costs of bushfire disasters, and bushfire fire management remains a poorly developed research frontier that demands collaboration of expertise from a broad cross‐section of fields that often have limited experience of collaborating together. The need for such synthetic thinking about fire's place on Earth has spawned the discipline of pyrogeography.
Organisational Capacity for Engaging with Indigenous Australians
Authors: HOWITT RICHARD , COLYER CLAIRE , HAMMER MITCHELL R. , HAVNEN OLGA , HUCHENDORF KAREN , HUBERT CAROL
Published: July 2014

Community capacity building is a common goal for programmes and policies involving Indigenous peoples, but it relies heavily on organisational capacity to work effectively in intercultural settings. This paper reviews the organisational capacity of the senior leaders of Australian Red Cross and institutional efforts to build a culturally appropriate and respectful organisation. It reports results from a survey of the organisation's leadership team and follow‐up interviews undertaken in 2010, reviews the challenges facing the organisation in working with Aboriginal and Torres Strait Islander Australians, and considers institutional progress in building internal capacity to lead change in working with Aboriginal and Torres Strait Islander Australians. The paper concludes with discussion of wider implications of this research.
Meteorological Sub‐divisional Scale Rainfall Monitoring Using Kalpana‐1 VHRR Measurements
Authors: MAHESH C. , PRAKASH S. , GAIROLA R.M. , SHAH S. , PAL P.K.
Published: July 2014

Geostationary satellites provide measurements over a wider geographical area with high temporal sampling, while microwave measurements are more accurate but sparse. For continuous monitoring of the Indian monsoon, geostationary platform would be ideal. In this study, INSAT (Indian National Satellite) Multi‐spectral Rainfall Algorithm (IMSRA) has been used for the estimation of rainfall from Kalpana‐1 very high resolution radiometer (VHRR) measurements. IMSRA benefits from the relative advantages of infrared and microwave sensors and is operational at the India Meteorological Department (IMD). In this paper, rainfall is estimated over India at meteorological sub‐divisional scale during the south‐west monsoon season of 2009 using Kalpana‐1 satellite measurements. This is the first experimental attempt to generate meteorological sub‐divisional scale rainfall maps using Kalpana‐1 satellite measurements. The rainfall maps for the south‐west monsoon season over the Indian land region are successfully utilised as a space input for the drought monitoring of the year 2009. The results have been compared with the IMD gauge‐based accumulated rainfall maps at monthly and seasonal time scales. The qualitative comparison suggests that rainfall maps generated using the present methodology is in good agreement with the IMD rainfall maps. The quantitative comparison of the sub‐divisional monthly accumulated rainfall shows a correlation of 0.77 and standard error of 71 mm over the non‐orographic regions, whereas a correlation of 0.60 and standard error of 117 mm is observed over the orographic regions. The present study shows that Kalpana‐1 satellite‐based rainfall estimates (IMSRA technique) can act as a complementary tool for the monsoon monitoring over the Indian meteorological sub‐divisions and can be used for various meteorological and hydrological applications.
Mapping 100 Years of Thornthwaite Moisture Index: Impact of Climate Change in Victoria, Australia
Authors: LEAO SIMONE
Published: July 2014

Geographer C. W. Thornthwaite proposed in 1948 a moisture index called Thornthwaite Moisture Index (TMI) as part of a water balance model for a new classification system for climate. The importance of TMI climatic classification has been recognised in many areas of knowledge and practice worldwide over the last 60 years. However, although past climate research was focused on developing adequate methods for climate classification, current research is more concerned with understanding the patterns of climate change. The use of TMI as an indicator for climate change is still an incipient area of research. The contributions of this paper are twofold. First, it is to fully document a methodology based on geostatistics adopted to produce a time series of TMI maps that are accurate and have high spatial resolution. The state of Victoria, in Australia, over the last century, is used as the case study. Second, by analysing these maps, the paper presents a general evaluation of the spatial patterns found in Victoria related to moisture variability across space and over time. Some potential implications of the verified moisture changes are discussed, and a number of ideas for further development are suggested.
Flavobacterium psychrophilum vaccine development: a difficult task
Authors: Gómez Esther , Méndez Jessica , Cascales Desirée , Guijarro José A.
Published: July 2014

Bacterial cold water disease (BCWD) is a globally distributed freshwater fish disease caused by the Gram‐negative bacterium Flavobacterium psychrophilum. It is a particularly devastating infection in fry salmonids and may lead to high levels of mortality. In spite of its economic impact on fish farms, neither the biology of the bacterium nor the bacterium–host interactions are well understood. This review provides a synopsis of the major problems related to critical remaining questions about research into the use of vaccines against F. psychrophilum and the development of a commercial vaccine against this disease. Studies using sera from convalescent rainbow trout have shown the antigenic properties of different proteins such as OmpH, OmpA and FspA, as well as low and high molecular mass lipopolysaccharide of F. psychrophilum, which are potential candidates for subunit vaccines. Inactivated F. psychrophilum bacterins have been successfully tested as vaccines under laboratory conditions by both immersion and intraperitoneal routes. However, the efficacy and the practical usefulness of these preparations still have to be proved. The use of attenuated and wild‐type strains to immunize fish showed that these systems offer high levels of protection. Nevertheless, their application clashes with the regulations for environmental protection in many countries. In conclusion, protective vaccines against BCWD are theoretically possible, but substantial efforts still have to be made in order to permit the development of a commercial vaccine.
Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA‐based diet analyses
Authors: Egeter Bastian , Bishop Phillip J. , Robertson Bruce C.
Published: July 2014

Amphibians are currently the most threatened group of vertebrates worldwide, and introduced fauna play a major role in their decline. The control of introduced predators to protect endangered species is often based on predation rates derived from diet studies of predators, but prey detection probabilities using different techniques are variable. We measured the detectability of frogs as prey, using morphological and DNA‐based diet analyses, in the stomachs and faeces of four mammal species that have been introduced to many areas of the world. Frogs (Litoria raniformis) were fed to rats (Rattus norvegicus and R. rattus), mice (Mus musculus) and hedgehogs (Erinaceus europaeus). DNA‐based analysis outperformed morphological analysis, increasing the prey detection rate from 2% to 70% in stomachs and from 0% to 53% in faeces. In most cases, utilizing either stomachs or faeces did not affect the success of prey DNA detection; however, using faeces extended the detectability half‐life from 7 to 21 h. This study is the first to measure prey DNA detection periods in mammalian stomachs, and the first to compare prey DNA detection periods in the stomachs and faeces of vertebrates. The results indicate that DNA‐based diet analysis provides a more reliable approach for detecting amphibians as prey and has the potential to be used to estimate the rate of predation by introduced mammals on endangered amphibians.
Clinical study on postoperative recurrence in patients with pN1 esophageal squamous cell carcinoma
Authors: Guo Xufeng , Mao Teng , Gu Zhitao , Ji Chunyu , Fang Wentao
Published: July 2014

Background

The 7th edition Union for International Cancer Control esophageal cancer staging system has changed the pathological N stage from N0, N1 (the existence state of regional lymph node metastasis) to N0, N1, N2, and N3 (number of regional lymph node metastasis). This study was designed to analyze the influencing factors of early recurrence in patients with pathological N1 stage (pN1 stage) esophageal squamous cell carcinoma (ESCC) after radical esophagectomy.

Method

A retrospective study of 95 consecutive pN1 stage ESCC patients was conducted. The Cox proportional hazards model was used to determine the independent risk factors for recurrence.

Results

Recurrence was recognized in 52 patients (54.7%) within three years after surgery. The median time to tumor recurrence was 14.2 months. Locoregional recurrence was found in 42 patients (44.2%) and hematogenous metastasis in 10 patients (10.5%). Recurrence closely correlated with pT stage, positive lymph node metastasis (LNM) in 2‐station and/or 2‐field, pathologic stage, intramural metastasis, lymph‐vascular invasion, and postoperative adjuvant chemotherapy (χ2 = 8.853∼65.695, P < 0.05). Cox multivariate analysis showed that pT3‐4a stage (odds ratio [OR] = 3.604, P = 0.027), positive LNM in 2‐station (OR = 4.834, P = 0.009) or 2‐field (OR = 5.689, P = 0.003) and no adjuvant chemotherapy (OR = 1.594, p = 0.048) were independent risk factors for postoperative recurrence.

Conclusion

Adjuvant chemotherapy might be helpful to reduce the recurrence rate of pN1 patients with thoracic ESCC. Induction therapy could further improve the therapeutic effect of pN1 ESCC with suspected multi‐station and/or multi‐field LNM.
Model‐based approaches to unconstrained ordination
Authors: Hui Francis K.C. , Taskinen Sara , Pledger Shirley , Foster Scott D. , Warton David I.
Published: July 2014

Unconstrained ordination is commonly used in ecology to visualize multivariate data, in particular, to visualize the main trends between different sites in terms of their species composition or relative abundance.

Methods of unconstrained ordination currently used, such as non‐metric multidimensional scaling, are algorithm‐based techniques developed and implemented without directly accommodating the statistical properties of the data at hand. Failure to account for these key data properties can lead to misleading results.

A model‐based approach to unconstrained ordination can address this issue, and in this study, two types of models for ordination are proposed based on finite mixture models and latent variable models. Each method is capable of handling different data types and different forms of species response to latent gradients. Further strengths of the models are demonstrated via example and simulation.

Advantages of model‐based approaches to ordination include the following: residual analysis tools for checking assumptions to ensure the fitted model is appropriate for the data; model selection tools to choose the most appropriate model for ordination; methods for formal statistical inference to draw conclusions from the ordination; and improved efficiency, that is model‐based ordination better recovers true relationships between sites, when used appropriately.
Caloric restriction reveals a metabolomic and lipidomic signature in liver of male mice
Authors: Jové Mariona , Naudí Alba , Ramírez‐Núñez Omar , Portero‐Otín Manuel , Selman Colin , Withers Dominic J. , Pamplona Reinald
Published: July 2014

Lipid composition, particularly membrane unsaturation, has been proposed as being a lifespan determinant, but it is currently unknown whether caloric restriction (CR), an accepted life‐extending intervention, affects cellular lipid profiles. In this study, we employ a liquid chromatography quadrupole time‐of‐flight‐based methodology to demonstrate that CR in the liver of male C57BL/6 mice: (i) induces marked changes in the cellular lipidome, (ii) specifically reduces levels of a phospholipid peroxidation product, 1‐palmitoyl‐2‐glutaryl‐sn‐glycero‐3‐phosphatidylcholine, (iii) alters cellular phosphoethanolamine and triglyceride distributional profiles, (iv) affects mitochondrial electron transport chain complexes, increasing complex II and decreasing complex III and (v) is associated with specific changes in liver metabolic pathways. These data demonstrate that CR induces a specific lipidome and metabolome reprogramming event in mouse liver which is associated with lower protein oxidative damage, as assessed by mass spectrometry‐based measurements. Such changes may be critical to the increased lifespan and healthspan observed in C57BL/6 mice following CR.