bluuebunny/crossref_metadata_2025 huggingface dataset:
minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers
Authors: Albanese Davide , Filosi Michele , Visintainer Roberto , Riccadonna Samantha , Jurman Giuseppe , Furlanello Cesare
Published: December 2012

Summary: We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks as well as on large ( = 1340) microarray and Illumina GAII RNA-seq transcriptomics datasets.

Availability and implementation: Source code and binaries are freely available for download under GPL3 licence at http://minepy.sourceforge.net for minepy and through the CRAN repository http://cran.r-project.org for the R package minerva. All software is multiplatform (MS Windows, Linux and OSX).

Contact:  furlan@fbk.eu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Sharing the Northeast Atlantic mackerel
Authors: Hannesson Rögnvaldur
Published: December 2012

The sharing of the Northeast Atlantic mackerel (Scomber scombrus) stock is analysed as a game between four parties: the European Union, Norway, the Faroe Islands, and Iceland. Consideration is given to how the outcome depends on the nature of the stock's migrations. Two types of migrations are considered: (i) density-dependent, where the mackerel migrates into the Icelandic economic zone only if it exceeds 3.5 million t, and (ii) stochastic migrations, where the said migrations are stochastic. It is determined that the Faroe Islands would never accept a cooperative solution wherein they can only fish with the globally optimal fishing mortality within their own zone. This is also true for Iceland when the migrations into her zone are stochastic, but not if they are density-dependent. In the latter case, the other players have incentives to retaliate to Icelandic overfishing by fishing harder, which greatly reduces the number of years when mackerel are available in the Icelandic zone. It is assumed that the objective is maximization of the catch volume over a time-horizon of 50 years.
Reasoning about Interference Between Units: A General Framework
Authors: Bowers Jake , Fredrickson Mark M. , Panagopoulos Costas
Published: December 2012

If an experimental treatment is experienced by both treated and control group units, tests of hypotheses about causal effects may be difficult to conceptualize, let alone execute. In this article, we show how counterfactual causal models may be written and tested when theories suggest spillover or other network-based interference among experimental units. We show that the “no interference” assumption need not constrain scholars who have interesting questions about interference. We offer researchers the ability to model theories about how treatment given to some units may come to influence outcomes for other units. We further show how to test hypotheses about these causal effects, and we provide tools to enable researchers to assess the operating characteristics of their tests given their own models, designs, test statistics, and data. The conceptual and methodological framework we develop here is particularly applicable to social networks, but may be usefully deployed whenever a researcher wonders about interference between units. Interference between units need not be an untestable assumption; instead, interference is an opportunity to ask meaningful questions about theoretically interesting phenomena.
‘Insect aquaplaning’ on a superhydrophilic hairy surface: howHeliamphora nutansBenth. pitcher plants capture prey
Authors: Bauer Ulrike , Scharmann Mathias , Skepper Jeremy , Federle Walter
Published: December 2012

Trichomes are a common feature of plants and perform important and diverse functions. Here, we show that the inward-pointing hairs on the inner wall of insect-trappingHeliamphora nutanspitchers are highly wettable, causing water droplets to spread rapidly across the surface. Wetting strongly enhanced the slipperiness and increased the capture rate for ants from 29 to 88 per cent. Force measurements and tarsal ablation experiments revealed that wetting affected the insects' adhesive pads but not the claws, similar to the ‘aquaplaning’ mechanism of (unrelated) AsianNepenthespitcher plants. The inward-pointing trichomes provided much higher traction when insects were pulled outwards. The wetness-dependent capture mechanisms ofH. nutansandNepenthespitchers present a striking case of functional convergence, whereas the use of wettable trichomes constitutes a previously unknown mechanism to make plant surfaces slippery.
Maribacter chungangensis sp. nov., isolated from a green seaweed, and emended descriptions of the genus

Maribacter

and

Maribacter arcticus
Authors: Weerawongwiwat Veeraya , Kang Hyeonji , Jung Min Young , Kim Wonyong
Published: December 2012

A Gram-stain-negative, non-spore-forming, strictly aerobic, orange-pigmented bacterial strain, motile by gliding, designated CAU 1044T, was isolated from a green seaweed and its taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CAU 1044T formed a distinct lineage within the genus

Maribacter

and was most closely related to

Maribacter antarcticus

JCM 15445T and

Maribacter arcticus

KOPRI 20941T (96.3 and 95.7 % similarity, respectively). Strain CAU 1044T contained menaquinone 6 as the only isoprenoid quinone and iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH), iso-C17 : 0 3-OH and iso-C15 : 1 G as the major fatty acids. The cell wall peptidoglycan of strain CAU 1044T contained meso-diaminopimelic acid and the major whole-cell sugars were glucose and ribose. The polar lipids were composed of phosphatidylethanolamine, one unidentified phospholipid, six unidentified aminolipids and four unidentified lipids. The DNA G+C content was 40.2 mol%. On the basis of phenotypic data and phylogenetic inference, strain CAU 1044T should be classified as a representative of a novel species in the genus

Maribacter

for which the name Maribacter chungangensis sp. nov. is proposed. The type strain is CAU 1044T ( = KCTC 23735T  = CCUG 61948T). Emended descriptions of the genus

Maribacter

and the species

M. arcticus

KCTC 22053T are also proposed.
Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove
Authors: Vashist Poonam , Nogi Yuichi , Ghadi Sanjeev C. , Verma Pankaj , Shouche Yogesh S.
Published: December 2012

A rod-shaped, Gram-negative, non-motile, aerobic and non-endospore forming bacterium, designated strain DD-13T, was isolated from the mangrove ecosystem of Goa, India. Strain DD-13T degraded polysaccharides such as agar, alginate, chitin, cellulose, laminarin, pectin, pullulan, starch, carrageenan, xylan and β-glucan. The optimum pH and temperature for growth was 7 and 36 °C, respectively. The strain grew optimally in the presence of 3 % NaCl (w/v). The DNA G+C content was 61.4 mol%. The predominant fatty acid of strain DD-13T was iso-C15 : 0. Ubiquinone-8 was detected as the major respiratory lipoquinone. Phylogenetic studies based on 16S rRNA gene sequence analysis demonstrated that strain DD-13T formed a coherent cluster with species of the genus

Microbulbifer

. Strain DD-13T exhibited 16S rRNA gene sequence similarity levels of 98.9–97.1 % with

Microbulbifer hydrolyticus

IRE-31T,

Microbulbifer salipaludis

JCM 11542T,

Microbulbifer agarilyticus

JAMB A3T,

Microbulbifer celer

KCTC 12973T and

Microbulbifer elongatus

DSM 6810T. However, the level of DNA–DNA relatedness between strain DD-13T and the five type strains of these species of the genus

Microbulbifer

were in the range of 26–33 %. Additionally, strain DD-13T demonstrates several phenotypic differences from these type strains of species of the genus

Microbulbifer

. Thus strain DD-13T represents a novel species of the genus

Microbulbifer

, for which the name Microbulbifer mangrovi sp. nov. is proposed with the type strain DD-13T ( = KCTC 23483T = JCM 17729T).
Bhargavaea

ullalensis sp. nov., isolated from coastal sand
Authors: Glaeser Stefanie P. , Arun A. B. , Rekha P. D. , Prabhu Sudharshan , Busse Hans-Jürgen , Kämpfer Peter
Published: December 2012

A Gram-positive-staining, aerobic, non-endospore-forming bacterium, isolated from Ullal coastal sand, Mangalore, Karnataka, India, on marine agar 2216, was studied in detail for its taxonomic position. Based on 16S rRNA gene sequence similarity comparisons, strain ZMA 19T was grouped into the genus

Bhargavaea

with high 16S rRNA gene sequence similarities to all currently described species of the genus

Bhargavaea

,

Bhargavaea cecembensis

(99.3 %),

Bhargavaea beijingensis

(98.8 %) and

Bhargavaea ginsengi

(98.6 %). GyrB amino acid sequence-based analysis supported the phylogenetic position and also distinguished strain ZMA 19T from the three other species of the genus

Bhargavaea

. Amino acid sequence similarities were only 85.6 to 89.5 % between strain ZMA 19T and the type strains of members of the genus

Bhargavaea

, which shared higher similarities among each other (93.0 to 96.2 %). The chemotaxonomic characterization supported the allocation of the novel strain to the genus

Bhargavaea

. The major menaquinone was MK-8. The polar lipid profile contained predominantly diphosphatidylglycerol and moderate amounts of phosphatidylglycerol. The diagnostic peptidoglycan diamino acid was lysine and the polyamine pattern contained spermidine and spermine. The major fatty acids were iso- and anteiso-branched fatty acids. DNA–DNA hybridization with the types strains

Bhargavaea cecembensis

LMG 24411T,

Bhargavaea beijingensis

DSM 19037T and

Bhargavaea ginsengi

DSM 19038T resulted in values (reciprocal values in parentheses) of 26 % (29 %), 18 % (15 %) and 21 % (12 %), respectively. The results of physiological and biochemical tests allowed phenotypic differentiation of strain ZMA 19T from all other species of the genus

Bhargavaea

. Thus, ZMA 19T represents a novel species of this genus, for which the name

Bhargavaea

ullalensis sp. nov. is proposed, with ZMA 19T ( = LMG 27071T  = CCM 8429T) as the type strain.
Tonsilliphilus suis gen. nov., sp. nov., causing tonsil infections in pigs
Authors: Azuma Ryozo , Ung-Bok Bak , Murakami Satoshi , Ishiwata Hiroyuki , Osaki Makoto , Shimada Nobuaki , Ito Yasuichiro , Miyagawa Eichi , Makino Takashi , Kudo Takuji , Takahashi Yoko , Yano Ikuya , Murata Ryo , Yokoyama Eiji
Published: December 2012

A micro-organism resembling members of the genusDermatophilus, strain W254T, which was isolated from the submandibular lymph node of a pig, and an additional 16 strains isolated from swine tonsils, were studied to establish their taxonomic status. Although all 17 strains were isolated anaerobically under an atmosphere of 100 % CO2, all of them were aerotolerant anaerobes. The micro-organisms showed at least five cellular morphologies: (i) a radially protrusive thallus, which proliferated into tuber-like cells; (ii) segmentation in both tubers and thallus followed by multilocule formation, (iii) development of coccoid forms in the locules; (iv) a change from the coccoid forms to zoospores; (v) resting cells, which were able to develop into protrusive thalli again. The micro-organisms were positive for nitrate reduction, but negative for catalase, indole production, hydrolysis of urea and gelatin liquefaction. Milk was not decomposed and none of the strains was haemolytic. A total of 16 compounds, including glucose, were utilized as sole carbon sources and seven compounds, includingl-arabinose, were not utilized. Three out of the 17 strains were subjected to further studies. The micro-organisms hadmeso-diaminopimelic acid in their peptidoglycan and galactose, glucose, madurose and a trace of mannose in their whole-cell sugar patterns. The major phospholipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol.Cellular fatty acids were C15 : 0(35.7–23.1 %), C16 : 0(5.9–2.4 %) C17 : 0(62.9–39.5 %), C17 : 1(24.4–0 %) and C18 : 0(3–1.6 %). The predominant menaquinone was MK-8 (H4). The G+C content of the DNA was 69.6–71.8 mol%. Analysis of the 16S rRNA gene sequences showed that the strains clustered with the type strains of members of the familyDermatophilaceae. Based on the polyphasic taxonomic characterization carried out, all 17 strains are considered to belong to a novel species in a new genus, for which the nameTonsilliphilus suisgen. nov., sp. nov. is proposed. The type strain of the type species is W254T( = ATCC 35846T = CCM 3774T = DSM 21880T = JCM 15727T).
Ruegeria intermedia sp. nov., a moderately thermophilic bacterium isolated from a coastal hot spring
Authors: Kämpfer P. , Arun A. B. , Rekha P. D. , Busse H.-J. , Young C.-C. , Glaeser S. P.
Published: December 2012

A cream-coloured, Gram-negative, aerobic, non-motile moderately thermophilic, rod-to-irregular-shaped bacterium, CC-GIMAT-2T, was isolated from a coastal hot spring of Green Island (Lutao), located off Taituang, Taiwan, on marine agar 2216. The 16S rRNA gene sequence analysis and subsequent comparisons showed that it was placed into the genus

Ruegeria

with 97.4 % similarity to

Ruegeria lacuscaerulensis

ITI-1157T, and a lower sequence similarity to all other species of the genus

Ruegeria

. Reconstruction of phylogenetic trees indicated that strain CC-GIMAT-2T clustered within the genus

Ruegeria

. Robust tree topology for the genus

Ruegeria

including the new strain was only obtained by including all

Rhodobacteraceae

type strains but not if the analysis was limited to few selected taxa. The quinone system contained exclusively ubiquinone Q-10 and the fatty acid profile consisted mainly of C18 : 1ω7c, 11-methyl C18 : 1ω7c and C12 : 0 3-OH. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminolipid. Other lipids were detected in moderate to minor amounts. The characteristic feature of the polyamine pattern was the predominant triamine spermidine. On the basis of the 16S rRNA gene sequence analysis and of the chemotaxonomic and physiological data, strain CC-GIMAT-2T represents a novel species of the genus

Ruegeria

, for which the name Ruegeria intermedia sp. nov. is proposed. The type strain is CC-GIMAT-2T ( = CCUG 59209T = LMG 25539T = CCM 7758T).
Streptosporangium sandarakinum sp. nov.
Authors: Kämpfer Peter , Glaeser Stefanie P. , Grün-Wollny Iris , Busse Hans-Jürgen
Published: December 2012

A Gram-positive, non-spore-forming bacterium (GW-12028T) of unknown origin showing filamentous growth and producing spherical sporangia was studied for its taxonomic allocation. The 16S rRNA gene sequence analysis and subsequent similarity studies showed that strain GW-12028T belongs to the genus

Streptosporangium

, and is most closely related to

Streptosporangium pseudovulgare

DSM 43181T (99.9 %) and

Streptosporangium nondiastaticum

DSM 43848T (99.6 %) and more distantly related to

Streptosporangium fragile

IFO 14311T (98.4 %) and other species of the genus

Streptosporangium

(95.8 to 98 %). Chemotaxonomic analyses showed that the peptidoglycan diamino acid was meso-diaminopimelic acid. Whole-cell hydrolysates contained madurose as the diagnostic sugar and exhibited a quinone system that contained predominantly menaquinones with nine isoprenoic units in the side chain [MK-9, MK-9(H2), MK-9(H4)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phoshatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannosides, four unidentified glycolipids, a phospholipid and an aminolipid. The polyamine pattern contained the major compounds spermine and spermidine. The major fatty acids were 10-methyl C17 : 0, iso-C16 : 0 and C15 : 0. These chemotaxonomic traits are common to other species of the genus

Streptosporangium

. DNA–DNA hybridizations and physiological and biochemical tests in comparison with the type strains of the most closely related species,

S. nondiastaticum

and

S. pseudovulgare

, allowed genotypic and phenotypic differentiation of strain GW-12028T. This strain represents a novel species, for which we propose the name Streptosporangium sandarakinum sp. nov., with the type strain GW-12028T ( = LMG 27062T  = DSM 45763T).
Caulobacter daechungensis sp. nov., a stalked bacterium isolated from a eutrophic reservoir
Authors: Jin Long , Lee Hyung-Gwan , Kim Hee-Sik , Ahn Chi-Yong , Oh Hee-Mock
Published: December 2012

A Gram-stain-negative, aerobic, non-spore-forming, curved, rod-shaped bacterium, H-E3-2T, was isolated from a water sample taken from Daechung Reservoir, Republic of Korea, during the late-blooming period of cyanobacteria. Strain H-E3-2T was motile with a single polar flagellum or non-motile (stalked cell). Comparative 16S rRNA gene sequence studies showed the isolate had a clear affiliation with the class

Alphaproteobacteria

and was most closely related to

Caulobacter fusiformis

ATCC 15257T and

Caulobacter mirabilis

LMG 24261T, showing 97.6 and 97.3 % 16S rRNA gene sequence similarity, respectively, and 95.3–96.3 % similarity to all other species of the genus

Caulobacter

. The predominant ubiquinone was Q-10. The major fatty acids were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0. The G+C content of the genomic DNA of strain H-E3-2T was 64.7 mol%. DNA–DNA hybridization values of strain H-E3-2T with

C. fusiformis

ATCC 15257T and

C. mirabilis

LMG 24261T were 21.2 and 19.7 %, respectively. Thus, based on the results of polyphasic analysis, it is proposed that strain H-E3-2T represents a novel species of the genus

Caulobacter

, for which the name Caulobacter daechungensis sp. nov. is proposed. The type strain is H-E3-2T ( = KCTC 32211T = JCM 18689T).
Cooperative Scheduling of Imaging Observation Tasks for High-Altitude Airships Based on Propagation Algorithm
Authors: Chuan He , Dishan Qiu , Jin Liu
Published: December 2012

The cooperative scheduling problem on high-altitude airships for imaging observation tasks is discussed. A constraint programming model is established by analyzing the main constraints, which takes the maximum task benefit and the minimum cruising distance as two optimization objectives. The cooperative scheduling problem of high-altitude airships is converted into a main problem and a subproblem by adopting hierarchy architecture. The solution to the main problem can construct the preliminary matching between tasks and observation resource in order to reduce the search space of the original problem. Furthermore, the solution to the sub-problem can detect the key nodes that each airship needs to fly through in sequence, so as to get the cruising path. Firstly, the task set is divided by using k-core neighborhood growth cluster algorithm (K-NGCA). Then, a novel swarm intelligence algorithm named propagation algorithm (PA) is combined with the key node search algorithm (KNSA) to optimize the cruising path of each airship and determine the execution time interval of each task. Meanwhile, this paper also provides the realization approach of the above algorithm and especially makes a detailed introduction on the encoding rules, search models, and propagation mechanism of the PA. Finally, the application results and comparison analysis show the proposed models and algorithms are effective and feasible.
Case Study on Incentive Mechanism of Energy Efficiency Retrofit in Coal-Fueled Power Plant in China
Authors: Yuan Donghai , Guo Xujing , Cao Yuan , He Liansheng , Wang Jinggang , Xi Beidou , Li Junqi , Ma Wenlin , Zhang Mingshun
Published: December 2012

An ordinary steam turbine retrofit project is selected as a case study; through the retrofit, the project activities will generate emission reductions within the power grid for about 92,463 tCO2e per annum. The internal rate of return (IRR) of the project is only −0.41% without the revenue of carbon credits, for example, CERs, which is much lower than the benchmark value of 8%. Only when the unit price of carbon credit reaches 125 CNY/tCO2, the IRR could reach the benchmark and an effective carbon tax needs to increase the price of carbon to 243 CNY/tce in order to make the project financially feasible. Design of incentive mechanism will help these low efficiency enterprises improve efficiency and reduce CO2emissions, which can provide the power plants sufficient incentive to implement energy efficiency retrofit project in existing coal-fuel power generation-units, and we hope it will make a good demonstration for the other low efficiency coal-fueled power generation units in China.
The E3 ligase APC/C–Cdh1 is required for associative fear memory and long-term potentiation in the amygdala of adult mice
Authors: Pick Joseph E. , Malumbres Marcos , Klann Eric
Published: December 2012

The anaphase promoting complex/cyclosome (APC/C) is an E3 ligase regulated by Cdh1. Beyond its role in controlling cell cycle progression, APC/C–Cdh1 has been detected in neurons and plays a role in long-lasting synaptic plasticity and long-term memory. Herein, we further examined the role of Cdh1 in synaptic plasticity and memory by generating knockout mice where Cdh1 was conditionally eliminated from the forebrain post-developmentally. Although spatial learning and memory in the Morris water maze (MWM) was normal, the Cdh1 conditional knockout (cKO) mice displayed enhanced reversal learning in the MWM and in a water-based Y maze. In addition, we found that the Cdh1 cKO mice had impaired associative fear memory and exhibited impaired long-term potentiation (LTP) in amygdala slices. Finally, we observed increased expression of Shank1 and NR2A expression in amygdalar slices from the Cdh1 cKO mice following the induction of LTP, suggesting a possible molecular mechanism underlying the behavioral and synaptic plasticity impairments displayed in these mice. Our findings are consistent with a role for the APC/C–Cdh1 in fear memory and synaptic plasticity in the amygdala.
Effects of aversive stimuli beyond defensive neural circuits: Reduced excitability in an identified neuron critical for feeding in Aplysia
Authors: Shields-Johnson Maria E. , Hernandez John S. , Torno Cody , Adams Katherine M. , Wainwright Marcy L. , Mozzachiodi Riccardo
Published: December 2012

In Aplysia, repeated trials of aversive stimuli produce long-term sensitization (LTS) of defensive reflexes and suppression of feeding. Whereas the cellular underpinnings of LTS have been characterized, the mechanisms of feeding suppression remained unknown. Here, we report that LTS training induced a long-term decrease in the excitability of B51 (a decision-making neuron in the feeding circuit) that recovered at a time point in which LTS is no longer observed (72 h post-treatment). These findings indicate B51 as a locus of plasticity underlying feeding suppression. Finally, treatment with serotonin to induce LTS failed to alter feeding and B51 excitability, suggesting that serotonin does not mediate the effects of LTS training on the feeding circuit.
Cholinergic modulation during acquisition of olfactory fear conditioning alters learning and stimulus generalization in mice
Authors: Pavesi Eloisa , Gooch Allison , Lee Elizabeth , Fletcher Max L.
Published: December 2012

We investigated the role of cholinergic neurotransmission in olfactory fear learning. Mice receiving pairings of odor and foot shock displayed fear to the trained odor the following day. Pretraining injections of the nicotinic antagonist mecamylamine had no effect on subsequent freezing, while the muscarinic antagonist scopolamine significantly reduced freezing. To test whether cholinergic manipulation affected fear generalization, mice were presented with odors similar to the trained odor. Generalization was increased following pretraining scopolamine, while the muscarinic agonist oxotremorine decreased generalization. These results suggest that muscarinic neurotransmission during the acquisition of olfactory association modulates both the strength and specificity of learning.
Transcriptional and Functional Classification of the GOLVEN/ROOT GROWTH FACTOR/CLE-Like Signaling Peptides Reveals Their Role in Lateral Root and Hair Formation
Authors: Fernandez Ana , Drozdzecki Andrzej , Hoogewijs Kurt , Nguyen Anh , Beeckman Tom , Madder Annemieke , Hilson Pierre
Published: December 2012

The GOLVEN (GLV)/ROOT GROWTH FACTORS/CLE-Like small signaling peptide family is encoded by 11 genes in Arabidopsis (Arabidopsis thaliana). Some of them have already been shown to control root meristem maintenance, auxin fluxes, and gravitropic responses. As a basis for the detailed analysis of their function, we determined the expression domains for each of the 11 GLV genes with promoter-reporter lines. Although they are collectively active in all examined plant parts, GLV genes have highly specific transcription patterns, generally restricted to very few cells or cell types in the root and shoot and in vegetative and reproductive tissues. GLV functions were further investigated with the comparative analysis of root phenotypes induced by gain- and loss-of-function mutants or in treatments with GLV-derived synthetic peptides. We identified functional classes that relate to the gene expression domains in the primary root and suggest that different GLV signals trigger distinct downstream pathways. Interestingly, GLV genes transcribed at the early stages of lateral root development strongly inhibited root branching when overexpressed. Furthermore, transcription patterns together with mutant phenotypes pointed to the involvement of GLV4 and GLV8 in root hair formation. Overall, our data suggest that nine GLV genes form three subgroups according to their expression and function within the root and offer a comprehensive framework to study the role of the GLV signaling peptides in plant development.
PYRABACTIN RESISTANCE1-LIKE8 Plays an Important Role for the Regulation of Abscisic Acid Signaling in Root
Authors: Antoni Regina , Gonzalez-Guzman Miguel , Rodriguez Lesia , Peirats-Llobet Marta , Pizzio Gaston A. , Fernandez Maria A. , De Winne Nancy , De Jaeger Geert , Dietrich Daniela , Bennett Malcom J. , Rodriguez Pedro L.
Published: December 2012

Abscisic acid (ABA) signaling plays a critical role in regulating root growth and root system architecture. ABA-mediated growth promotion and root tropic response under water stress are key responses for plant survival under limiting water conditions. In this work, we have explored the role of Arabidopsis (Arabidopsis thaliana) PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS for root ABA signaling. As a result, we discovered that PYL8 plays a nonredundant role for the regulation of root ABA sensitivity. Unexpectedly, given the multigenic nature and partial functional redundancy observed in the PYR/PYL family, the single pyl8 mutant showed reduced sensitivity to ABA-mediated root growth inhibition. This effect was due to the lack of PYL8-mediated inhibition of several clade A phosphatases type 2C (PP2Cs), since PYL8 interacted in vivo with at least five PP2Cs, namely HYPERSENSITIVE TO ABA1 (HAB1), HAB2, ABA-INSENSITIVE1 (ABI1), ABI2, and PP2CA/ABA-HYPERSENSITIVE GERMINATION3 as revealed by tandem affinity purification and mass spectrometry proteomic approaches. We also discovered that PYR/PYL receptors and clade A PP2Cs are crucial for the hydrotropic response that takes place to guide root growth far from regions with low water potential. Thus, an ABA-hypersensitive pp2c quadruple mutant showed enhanced hydrotropism, whereas an ABA-insensitive sextuple pyr/pyl mutant showed reduced hydrotropic response, indicating that ABA-dependent inhibition of PP2Cs by PYR/PYLs is required for the proper perception of a moisture gradient.
LnIs a Key Regulator of Leaflet Shape and Number of Seeds per Pod in Soybean
Authors: Jeong Namhee , Suh Su Jeoung , Kim Min-Hee , Lee Seukki , Moon Jung-Kyung , Kim Hong Sig , Jeong Soon-Chun
Published: December 2012

Narrow leaflet soybean (Glycine max) varieties tend to have more seeds per pod than broad leaflet varieties. Narrow leaflet in soybean is conferred by a single recessive gene, ln. Here, we show that the transition from broad (Ln) to narrow leaflet (ln) is associated with an amino acid substitution in the EAR motif encoded by a gene (designated Gm-JAGGED1) homologous to Arabidopsis JAGGED (JAG) that regulates lateral organ development and the variant exerts a pleiotropic effect on fruit patterning. The genomic region that regulates both the traits was mapped to a 12.6-kb region containing only one gene, Gm-JAG1. Introducing the Gm-JAG1 allele into a loss-of-function Arabidopsis jagged mutant partially restored the wild-type JAG phenotypes, including leaf shape, flower opening, and fruit shape, but the Gm-jag1 (ln) and EAR-deleted Gm-JAG1 alleles in the jagged mutant did not result in an apparent phenotypic change. These observations indicate that despite some degree of functional change of Gm-JAG1 due to the divergence from Arabidopsis JAG, Gm-JAG1 complemented the functions of JAG in Arabidopsis thaliana. However, the Gm-JAG1 homoeolog, Gm-JAG2, appears to be sub- or neofunctionalized, as revealed by the differential expression of the two genes in multiple plant tissues, a complementation test, and an allelic analysis at both loci.
Relocalization of Late Blight Resistance Protein R3a to Endosomal Compartments Is Associated with Effector Recognition and Required for the Immune Response
Authors: Engelhardt Stefan , Boevink Petra C. , Armstrong Miles R. , Ramos Maria Brisa , Hein Ingo , Birch Paul R.J.
Published: December 2012

An important objective of plant–pathogen interactions research is to determine where resistance proteins detect pathogen effectors to mount an immune response. Many nucleotide binding–Leucine-rich repeat (NB-LRR) resistance proteins accumulate in the plant nucleus following effector recognition, where they initiate the hypersensitive response (HR). Here, we show that potato (Solanum tuberosum) resistance protein R3a relocates from the cytoplasm to endosomal compartments only when coexpressed with recognized Phytophthora infestans effector form AVR3aKI and not unrecognized form AVR3aEM. Moreover, AVR3aKI, but not AVR3aEM, is also relocalized to endosomes in the presence of R3a. Both R3a and AVR3aKI colocalized in close physical proximity at endosomes in planta. Treatment with brefeldin A (BFA) or wortmannin, inhibitors of the endocytic cycle, attenuated both the relocalization of R3a to endosomes and the R3a-mediated HR. No such effect of these inhibitors was observed on HRs triggered by the gene-for-gene pairs Rx1/PVX-CP and Sto1/IpiO1. An R3a(D501V) autoactive MHD mutant, which triggered HR in the absence of AVR3aKI, failed to localize to endosomes. Moreover, BFA and wortmannin did not alter cell death triggered by this mutant. We conclude that effector recognition and consequent HR signaling by NB-LRR resistance protein R3a require its relocalization to vesicles in the endocytic pathway.
BRK1, a Bub1-Related Kinase, Is Essential for Generating Proper Tension between Homologous Kinetochores at Metaphase I of Rice Meiosis
Authors: Wang Mo , Tang Ding , Luo Qiong , Jin Yi , Shen Yi , Wang Kejian , Cheng Zhukuan
Published: December 2012

Bub1 (for budding uninhibited by benzimidazole 1), one of the main spindle checkpoint kinases, acts as a kinetochore scaffold for assembling other checkpoint proteins. Here, we identify a plant Bub1-related kinase 1 (BRK1) in rice (Oryza sativa). The brk1 mutants are sterile due to the precocious separation of sister chromatids at the onset of anaphase I. The centromeric recruitment of SHUGOSHIN1 and phosphorylation of histone H2A at Thr-134 (H2A-pT134) depend on BRK1. Although the homologs can faithfully separate from each other at the end of meiosis I, the uncorrected merotelic attachment of paired sister kinetochores at the early stage of metaphase I in brk1 reduces the tension across homologous kinetochores, causes the metaphase I spindle to be aberrantly shaped, and subsequently affects the synchronicity of homolog separation at the onset of anaphase I. In addition, the phosphorylation of inner centromeric histone H3 at Ser-10 (H3-pS10) during diakinesis depends on BRK1. Therefore, we speculate that BRK1 may be required for normal localization of Aurora kinase before the onset of metaphase I, which is responsible for correcting the merotelic attachment.
WRINKLED Transcription Factors Orchestrate Tissue-Specific Regulation of Fatty Acid Biosynthesis in Arabidopsis
Authors: To Alexandra , Joubès Jérôme , Barthole Guillaume , Lécureuil Alain , Scagnelli Aurélie , Jasinski Sophie , Lepiniec Loïc , Baud Sébastien
Published: December 2012

Acyl lipids are essential constituents of all cells, but acyl chain requirements vary greatly and depend on the cell type considered. This implies a tight regulation of fatty acid production so that supply fits demand. Isolation of the Arabidopsis thaliana WRINKLED1 (WRI1) transcription factor established the importance of transcriptional regulation for modulating the rate of acyl chain production. Here, we report the isolation of two additional regulators of the fatty acid biosynthetic pathway, WRI3 and WRI4, which are closely related to WRI1 and belong to the APETALA2–ethylene-responsive element binding protein family of transcription factors. These three WRIs define a family of regulators capable of triggering sustained rates of acyl chain synthesis. However, expression patterns of the three WRIs differ markedly. Whereas only WRI1 activates fatty acid biosynthesis in seeds for triacylglycerol production, the three WRIs are required in floral tissues to provide acyl chains for cutin biosynthesis and prevent adherence of these developing organs and subsequent semisterility. The targets of these WRIs encode enzymes providing precursors (acyl chain and glycerol backbones) for various lipid biosynthetic pathways, but not the subsequent lipid-assembling enzymes. These results provide insights into the developmental regulation of fatty acid production in plants.
Pectin Biosynthesis: GALS1 in Arabidopsis thaliana Is a β-1,4-Galactan β-1,4-Galactosyltransferase
Authors: Liwanag April Jennifer Madrid , Ebert Berit , Verhertbruggen Yves , Rennie Emilie A. , Rautengarten Carsten , Oikawa Ai , Andersen Mathias C.F. , Clausen Mads H. , Scheller Henrik Vibe
Published: December 2012

β-1,4-Galactans are abundant polysaccharides in plant cell walls, which are generally found as side chains of rhamnogalacturonan I. Rhamnogalacturonan I is a major component of pectin with a backbone of alternating rhamnose and galacturonic acid residues and side chains that include α-1,5-arabinans, β-1,4-galactans, and arabinogalactans. Many enzymes are required to synthesize pectin, but few have been identified. Pectin is most abundant in primary walls of expanding cells, but β-1,4-galactan is relatively abundant in secondary walls, especially in tension wood that forms in response to mechanical stress. We investigated enzymes in glycosyltransferase family GT92, which has three members in Arabidopsis thaliana, which we designated GALACTAN SYNTHASE1, (GALS1), GALS2 and GALS3. Loss-of-function mutants in the corresponding genes had a decreased β-1,4-galactan content, and overexpression of GALS1 resulted in plants with 50% higher β-1,4-galactan content. The plants did not have an obvious growth phenotype. Heterologously expressed and affinity-purified GALS1 could transfer Gal residues from UDP-Gal onto β-1,4-galactopentaose. GALS1 specifically formed β-1,4-galactosyl linkages and could add successive β-1,4-galactosyl residues to the acceptor. These observations confirm the identity of the GT92 enzyme as β-1,4-galactan synthase. The identification of this enzyme could provide an important tool for engineering plants with improved bioenergy properties.
Working life and physical activity in ankylosing spondylitis pre and post anti‐tumor necrosis factor‐alpha therapy
Authors: Prince David S. , McGuigan Louis E. , McGirr Ellen E.
Published: December 2012

Aim

To assess effects of ankylosing spondylitis (AS) on working life and physical activity in Australia; to quantify changes in working life and physical activity that occur after anti‐tumor necrosis factor‐alpha (TNF‐α) treatment; and to assess efficacy of anti‐TNF‐α therapy for AS in an Australian context.

Methods

This is a multi‐centre observational study of people with AS on anti‐TNF‐α therapy. All participants satisfied the New York Modified Criteria and had active and refractory disease at anti‐TNF‐α therapy commencement. Participation involved a standardized interview, a metrology assessment, assessment of disease remission and medical record review. Interviews and patients' records were used to compare working life (employment, sick leave and productivity) and physical activity (participation rate, hours/week, and physical intensity) between the pre‐AS, post‐AS and post‐anti‐TNF‐α therapy periods.

Results

Fifty‐two patients took part. Participants were on average 44.8 years old, predominately male (86.5%) and had been on anti‐TNF‐α therapy for 29 months; 39% were in partial remission and 75% had 50% reduction in the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI). Responders to anti‐TNF‐α therapy were 10.5 years younger than non‐responders (P = 0.004). Post‐anti‐TNF‐α therapy participants gained 6.6 h/week of work (P = 0.02), and productivity improved 31% (P < 0.001) compared to immediately prior to commencing treatment. Physical activity participation increased from 71% to 85% (P = 0.039) and activity intensity increased by 33% (P = 0.002) post‐treatment. Participants gained 1.8 h/week of sport (P = 0.001) and 2.2 h/week of recreational physical activity (P < 0.001).

Conclusions

Australians with AS have their working life and physical activity severely affected by this disease. Treatment with anti‐TNF‐α therapy results in significant improvement in these parameters.
Elevated KIAA0101 expression is a marker of recurrence in human gastric cancer
Authors: Zhu Kun , Diao Dongmei , Dang Chengxue , Shi Lei , Wang Jianguang , Yan Rong , Yuan Dawei , Li Kang
Published: December 2012

Gastric cancer (GC) is one of the most common malignant tumors with a high rate of recurrence, which results in surgery being unsuccessful. Therefore, it is important to find the reason for the surgery failing. The purpose of the present study was to investigate a factor related to recurrence. Expression of KIAA0101 was assessed in 61 paired human primary GC and non‐cancerous gastric tissue using immunohistochemistry. After surgery, all 61 patients were followed regularly for more than 24 months or until death to analyze the 2‐year survival rate and recurrence. After suppressing KIAA0101 by RNA interference in human GC cell lines, the cell viability was detected using MTT. We are first to find that KIAA0101 was elevated in GC tissues compared with paired non‐cancerous gastric tissues. Immunohistochemical staining also revealed the predominant nuclear localization of KIAA0101 protein. Despite these findings, GC patients with elevated KIAA0101 expression levels exhibited a high recurrence and subsequently poor prognosis in the survival study. Also, cell viability was significantly inhibited after suppressing KIAA0101 in GC cells, suggesting that KIAA0101 might promote cancer cell proliferation. KIAA0101 is increased in human GC and is a marker of recurrence.
Early growth of environmental plantings in relation to site and management factors
Authors: England Jacqueline R. , Franks Emma J. , Weston Christopher J. , Polglase Philip J.
Published: December 2012

In extensively cleared areas of temperate Australia, large‐scale mixed‐species environmental revegetation is often recommended to address land and water degradation in rural landscapes. Although survival and growth are central to the success of revegetation, there is very limited information on this aspect of practice. We investigated how site and management practices influence early growth by surveying 29 planted or direct‐seeded sites, covering ages from 3–6 years, in north central Victoria, Australia. We measured heights and crown widths of trees and shrubs at each site and estimated average growth over time at the scale of: (i) individual trees or shrubs (mean height increment) and (ii) stand (vegetation cover increment and a ‘height integral’ increment variable, which integrates differences in both height and stand density). Relationships between growth increment variables and site factors, including climate, site preparation and land‐use history, were investigated to identify the main factors influencing early growth rates. Mean annual increment in height of individual trees was significantly higher for trees established from tubestock than those from direct seeding. Multiple linear regression models for two growth variables, cover increment and height integral increment, explained 61% and 38% of the variation, respectively, but with high uncertainty. Ploughing, pre‐establishment weed control and fertiliser addition improved growth rates. Revegetation method had a significant effect on early growth; at the scale of individuals, growth rates were higher for planted tubestock than for direct seeding, while at the stand scale, growth rates were higher for direct seeding than for planted tubestock.
Determination of Thallium in the USGS Glass Reference Materials BIR‐1G, BHVO‐2G and BCR‐2G and Application to Quantitative Tl Concentrations by LA‐ICP‐MS
Authors: Nielsen Sune G. , Lee Cin‐Ty A.
Published: December 2012

Here, we present determinations of thallium (Tl) concentrations in the USGS reference materials BIR‐1G, BHVO‐2G and BCR‐2G measured by solution ICP‐MS. The Tl content in these three glasses spans a range of about 2–230 ng g−1, which is similar to the values published for the respective powder materials. The determined range of Tl concentrations in these three glass reference materials makes them ideal for investigating Tl concentrations in basaltic and andesitic volcanic glasses. We also performed a series of laser ablation ICP‐MS measurements on the three samples, which show that this technique is able to determine Tl concentrations in glass samples with concentrations as low as 2 ng g−1.
Response of Sorghum to Abiotic Stresses: A Review
Authors: Tari I. , Laskay G. , Takács Z. , Poór P.
Published: December 2012

Sorghum [(Sorghum bicolor L.) Moench] is a highly productive crop plant, which can be used for alternative energy resource, human food, livestock feed or industrial purposes. The biomass of sorghum can be utilized as solid fuel via thermochemical routes or as a carbohydrate substrate via fermentation processes. The plant has a great adaptation potential to drought, high salinity and high temperature, which are important characteristics of genotypes growing in extreme environments. However, the climate change in the 21st century may bring about new challenges in the cultivated areas. In this review, we summarize the most recent literature about the responses of sorghum to the most important abiotic stresses: nutrient deficiency, aluminium stress, drought, high salinity, waterlogging or temperature stress the plants have to cope with during cultivation. The advanced molecular and system biological tools provide new opportunities for breeders to select stress‐tolerant and high‐yielding cultivars.
Delving intoDeliasHübner (Lepidoptera: Pieridae): fine‐scale biogeography, phylogenetics and systematics of the world's largest butterfly genus
Authors: Müller Chris J. , Matos‐Maraví Pável F. , Beheregaray Luciano B.
Published: December 2012

Aim

Our objective was to reconstruct a species‐level phylogeny of the genusDelias, to elucidate their finer‐scale biogeography and to test boundaries between closely related taxa.

Location

Indo‐Australian region, with a focus on Wallacea.

Methods

Sequence data from 131 taxa, representing all recognized species groups and more than half of the known species ofDelias, were used in the analysis. Phylogenetic analyses based on molecular characters of the mitochondrial gene cytochromecoxidase subunit I (COI) and nuclear geneswinglessand elongation factor 1α (EF‐1α) were carried out using maximum parsimony and Bayesian inference. Biogeographical reconstructions were undertaken using the parsimony‐based method dispersal–vicariance analysis and the dispersal–extinction–cladogenesis model as implemented inraspandLagrange, respectively.

Results

The phylogenetic hypothesis resolved 14 distinct clades, here designated thenysa,isse,pasithoe,belladonna,ladas,geraldina,aroae,eichhorni,sagessa,aganippe,hyparete,belisama,albertisiandnigrinaspecies groups.Delias blancaFelder andDelias chrysomelaenaSnellen van Vollenhoven were transferred to thepasithoeandissespecies groups, respectively. We demonstrate that the barcode region ofCOIis useful for the delineation of closely related, more recently diverged,Deliasspecies. Species diversification inDelias, for the most part, is shown to pre‐date the Pleistocene, even in montane mainland New Guinea where numerous phenotypically similar sister species co‐occur.

Main conclusions

SiblingDeliasspecies found in sympatry are largely restricted to those clades confined to mainland New Guinea, where most species occur in high‐elevation habitats. Conversely, clades with large geographical ranges are composed of essentially allopatric taxa. Although an Australian Plate origin is plausible for the genus,Deliasis likely to have colonized islands peripheral to Australia during the early stages of its evolution (i.e. during the Miocene), as evidenced by the presence of older lineages in Wallacea and also in islands of the south‐western Pacific.