bluuebunny/crossref_metadata_2025 huggingface dataset:
Mineral supplementation of lambing ewes grazing dual-purpose wheat
Authors: McGrath S. R. , Bhanugopan M. S. , Dove H. , Clayton E. H. , Virgona J. M. , Friend M. A.
Published: February 2014

Lambing ewes were grazed on dual-purpose wheat in two experiments in 2010 and 2011 with or without access to a mineral supplement. The calcium, magnesium and sodium content of wheat forage was below the requirements of ewes during late pregnancy and lactation; however, no clinical cases of hypocalcaemia or hypomagnesaemia were observed in either experiment. Blood serum assays identified eight hypocalcaemic ewes and one hypomagnesaemic ewe in Experiment 1, and one hypocalcaemic ewe in Experiment 2, and the provision of a mineral supplement comprising of magnesium oxide, calcium carbonate and coarse salt had no effect on blood magnesium, total calcium, phosphorus or sodium. Lamb birthweight and survival were not affected by provision of the mineral supplement in either experiment; however, the growth rate to marking (mean 38 ± 10 days of age) of twin-born lambs was higher in Experiment 1 when the supplement was provided to ewes grazing wheat (259 vs 243 g/head.day; P = 0.002).
Industry benefits from using genomic information in two- and three-tier sheep breeding systems
Authors: Horton B. J. , Banks R. G. , van der Werf J. H. J.
Published: February 2014

A model of the sheep breeding industry with nucleus flocks, multiplier flocks and commercial sheep flocks was used to examine the value of genomic selection. The model reflected a dual-purpose Merino breeding objective, with genomic information improving selection accuracy by 39% for rams at 6 months of age and by 17% at 18 months. The current level of net dollar benefit to the sheep industry from selection, but without genomic testing, can be improved by 10–14% for a closed three-tiered breeding structure with rams used at 18 months. If the rams are first used at 6–7 months then the dollar gains can be improved by 15–17%, since genomic information can provide proportionately greater gains for young animals that have limited phenotypic information. In a two-tiered breeding system, with nucleus flocks selling rams direct to commercial producers, rather than through multiplier flocks, the dollar gains to industry from genomic testing increased to ~12–13% for rams bred at 18 months, and 20–22% if nucleus rams are used at 6–7 months. The optimal structure requires two-stage selection, with an initial selection based on information available without genomic testing, to limit the cost of testing to only the superior rams. However, the optimum proportion of rams tested depends on the system and the cost of testing. In order to recover the cost of genomic testing, the nucleus flocks must recover up to 5% of the extra genetic gain as extra profit from sale of rams to commercial sheep producers.
Influence of cardamom essential oils and seeds on growth performance, blood characteristics and immunity of broilers
Authors: Omidi Mosa , Taherpour Kamran , Cheraghi Javad , Ghasemi Hossein A.
Published: February 2014

This study was conducted to investigate the impact of dietary supplementation of cardamom essential oils (CEO) and powdered cardamom seeds (PCS) on the growth performance, plasma biochemistry, haematological characters, immune response and meat acceptability in broilers. In total, 300 day-old male broilers (Ross 308) were allocated to five treatments with six replicates. Dietary treatments included the basal diet as control, CEO-supplemented diets with an inclusion level of 50 (CEO1) or 100 (CEO2) mg/kg, and PCS-supplemented diets with an inclusion level of 3 (PCS1) or 6 (PCS2) g/kg. Feeding PCS1 diet improved (P < 0.05) bodyweight gain and feed conversion ratio (FCR) of broilers during the grower period (11–28 days). Moreover, broilers fed the CEO2 diet had the lowest (P < 0.05) FCR during the whole growth period (0–42 days). Higher bursa index (P < 0.05) was detected in chickens receiving CEO1 and CEO2 diets; additionally, higher spleen index (P < 0.05) was recorded in the CEO1 group at 42 days of age. Haematological parameters including red blood cell, white blood cell, haemoglobin, haematocrit, mean corpuscular volume, mean corpuscular haemoglobin, and mean corpuscular haemoglobin concentration values were not influenced (P > 0.05) by diet. By contrast, CEO1 and CEO2 diets decreased (P < 0.05) the low-density lipoprotein cholesterol (LDL-C) concentrations compared with control diet. Plasma cholesterol level was also lower (P < 0.05) in the CEO1 group at 42 days of age. Sensory evaluation of meat samples indicated no differences (P > 0.05) among treatments for appearance, flavour, texture and overall acceptability. Our results suggest that the CEO2 diet was advantageous compared with control diet with respect to feed efficiency. Moreover, CEO1 had a positive effect on the blood cholesterol profile by decreasing the plasma cholesterol and LDL-C levels.
Epitope-specific antibody response is controlled by immunoglobulin VH polymorphisms
Authors: Raposo Bruno , Dobritzsch Doreen , Ge Changrong , Ekman Diana , Xu Bingze , Lindh Ingrid , Förster Michael , Uysal Hüseyin , Nandakumar Kutty Selva , Schneider Gunter , Holmdahl Rikard
Published: February 2014

Autoantibody formation is essential for the development of certain autoimmune diseases like rheumatoid arthritis (RA). Anti-type II collagen (CII) antibodies are found in RA patients; they interact with cartilage in vivo and are often highly pathogenic in the mouse. Autoreactivity to CII is directed to multiple epitopes and conserved between mice and humans. We have previously mapped the antibody response to CII in a heterogeneous stock cohort of mice, with a strong association with the IgH locus. We positioned the genetic polymorphisms and determined the structural requirements controlling antibody recognition of one of the major CII epitopes. Polymorphisms at positions S31R and W33T of the associated variable heavy chain (VH) allele were identified and confirmed by gene sequencing. The Fab fragment binding the J1 epitope was crystallized, and site-directed mutagenesis confirmed the importance of those two variants for antigen recognition. Back mutation to germline sequence provided evidence for a preexisting recognition of the J1 epitope. These data demonstrate a genetic association of epitope-specific antibody responses with specific VH alleles, and it highlights the importance of germline-encoded antibodies in the pathogenesis of antibody-mediated autoimmune diseases.
Neuronal activity regulates extracellular tau in vivo
Authors: Yamada Kaoru , Holth Jerrah K. , Liao Fan , Stewart Floy R. , Mahan Thomas E. , Jiang Hong , Cirrito John R. , Patel Tirth K. , Hochgräfe Katja , Mandelkow Eva-Maria , Holtzman David M.
Published: February 2014

Tau is primarily a cytoplasmic protein that stabilizes microtubules. However, it is also found in the extracellular space of the brain at appreciable concentrations. Although its presence there may be relevant to the intercellular spread of tau pathology, the cellular mechanisms regulating tau release into the extracellular space are not well understood. To test this in the context of neuronal networks in vivo, we used in vivo microdialysis. Increasing neuronal activity rapidly increased the steady-state levels of extracellular tau in vivo. Importantly, presynaptic glutamate release is sufficient to drive tau release. Although tau release occurred within hours in response to neuronal activity, the elimination rate of tau from the extracellular compartment and the brain is slow (half-life of ∼11 d). The in vivo results provide one mechanism underlying neuronal tau release and may link trans-synaptic spread of tau pathology with synaptic activity itself.
Transgenic kallikrein 5 mice reproduce major cutaneous and systemic hallmarks of Netherton syndrome
Authors: Furio Laetitia , de Veer Simon , Jaillet Madeleine , Briot Anais , Robin Aurelie , Deraison Celine , Hovnanian Alain
Published: February 2014

Netherton syndrome (NS) is a severe genetic skin disease in which absence of a key protease inhibitor causes congenital exfoliative erythroderma, eczematous-like lesions, and atopic manifestations. Several proteases are overactive in NS, including kallikrein-related peptidase (KLK) 5, KLK7, and elastase-2 (ELA2), which are suggested to be part of a proteolytic cascade initiated by KLK5. To address the role of KLK5 in NS, we have generated a new transgenic murine model expressing human KLK5 in the granular layer of the epidermis (Tg-KLK5). Transgene expression resulted in increased proteolytic activity attributable to KLK5 and its downstream targets KLK7, KLK14, and ELA2. Tg-KLK5 mice developed an exfoliative erythroderma with scaling, growth delay, and hair abnormalities. The skin barrier was defective and the stratum corneum was detached through desmosomal cleavage. Importantly, Tg-KLK5 mice displayed cutaneous and systemic hallmarks of severe inflammation and allergy with pruritus. The skin showed enhanced expression of inflammatory cytokines and chemokines, infiltration of immune cells, and markers of Th2/Th17/Th22 T cell responses. Moreover, serum IgE and Tslp levels were elevated. Our study identifies KLK5 as an important contributor to the NS proteolytic cascade and provides a new and viable model for the evaluation of future targeted therapies for NS or related diseases such as atopic dermatitis.
Extragalactic science, cosmology, and Galactic archaeology with the Subaru Prime Focus Spectrograph
Authors: Takada Masahiro , Ellis Richard S. , Chiba Masashi , Greene Jenny E. , Aihara Hiroaki , Arimoto Nobuo , Bundy Kevin , Cohen Judith , Doré Olivier , Graves Genevieve , Gunn James E. , Heckman Timothy , Hirata Christopher M. , Ho Paul , Kneib Jean-Paul , Fèvre Olivier Le , Lin Lihwai , More Surhud , Murayama Hitoshi , Nagao Tohru , Ouchi Masami , Seiffert Michael , Silverman John D. , Sodré Laerte , Spergel David N. , Strauss Michael A. , Sugai Hajime , Suto Yasushi , Takami Hideki , Wyse Rosemary
Published: February 2014

The Subaru Prime Focus Spectrograph (PFS) is a massively multiplexed fiber-fed optical and near-infrared three-arm spectrograph (Nfiber = 2400, 380 ≤ λ ≤ 1260 nm, 1 $_{.}^{\circ}$3 diameter field of view). Here, we summarize the science cases in terms of provisional plans for a 300-night Subaru survey. We describe plans to constrain the nature of dark energy via a survey of emission line galaxies spanning a comoving volume of 9.3 h−3 Gpc3 in the redshift range 0.8 < z < 2.4. In each of six redshift bins, the cosmological distances will be measured to 3% precision via the baryonic acoustic oscillation scale, and redshift-space distortion measures will constrain structure growth to 6% precision. In the near-field cosmology program, radial velocities and chemical abundances of stars in the Milky Way and M 31 will be used to infer the past assembly histories of spiral galaxies and the structure of their dark matter halos. Data will be secured for 106 stars in the Galactic thick-disk, halo, and tidal streams as faint as V ∼ 22, including stars with V < 20 to complement the goals of the Gaia mission. A medium-resolution mode with R = 5000 to be implemented in the red arm will allow the measurement of multiple α-element abundances and more precise velocities for Galactic stars. For the galaxy evolution program, our simulations suggest the wide wavelength range of PFS will be powerful in probing the galaxy population and its clustering over a wide redshift range. We plan to conduct a color-selected survey of 1 < z < 2 galaxies and AGN over 16 deg2 to J ≃ 23.4, yielding a fair sample of galaxies with stellar masses above ∼1010 M⊙ at z ≃ 2. A two-tiered survey of higher redshift Lyman break galaxies and Lyman alpha emitters will quantify the properties of early systems close to the reionization epoch.
The Degenerate EAL-GGDEF Domain Protein Filp Functions as a Cyclic di-GMP Receptor and Specifically Interacts with the PilZ-Domain Protein PXO_02715 to Regulate Virulence in Xanthomonas oryzae pv. oryzae
Authors: Yang Fenghuan , Tian Fang , Li Xiaotong , Fan Susu , Chen Huamin , Wu Maosen , Yang Ching-Hong , He Chenyang
Published: February 2014

Degenerate GGDEF and EAL domain proteins represent major types of cyclic diguanylic acid (c-di-GMP) receptors in pathogenic bacteria. Here, we characterized a FimX-like protein (Filp) which possesses both GGDEF and EAL domains in Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight of rice. Both in silico analysis and enzyme assays indicated that the GGDEF and EAL domains of Filp were degenerate and enzymatically inactive. However, Filp bound to c-di-GMP efficiently within the EAL domain, where Q477, E653, and F654 residues were crucial for the binding. Deletion of the filp gene in X. oryzae pv. oryzae resulted in attenuated virulence in rice and reduced type III secretion system (T3SS) gene expression. Complementation analysis with different truncated proteins indicated that REC, PAS, and EAL domains but not the GGDEF domain were required for the full activity of Filp in vivo. In addition, a PilZ-domain protein (PXO_02715) was identified as a Filp interactor by yeast two-hybrid and glutathione-S-transferase pull-down assays. Deletion of the PXO_02715 gene demonstrated changes in bacterial virulence and T3SS gene expression similar to Δfilp. Moreover, both mutants were impaired in their ability to induce hypersensitive response in nonhost plants. Thus, we concluded that Filp was a novel c-di-GMP receptor of X. oryzae pv. oryzae, and its function to regulate bacterial virulence expression might be via the interaction with PXO_02715.
Transmission of Pantoea ananatis and P. agglomerans, Causal Agents of Center Rot of Onion (Allium cepa), by Onion Thrips (Thrips tabaci) Through Feces
Authors: Dutta B. , Barman A. K. , Srinivasan R. , Avci U. , Ullman D. E. , Langston D. B. , Gitaitis R. D.
Published: February 2014

Frankliniella fusca, the tobacco thrips, has been shown to acquire and transmit Pantoea ananatis, one of the causal agents of the center rot of onion. Although Thrips tabaci, the onion thrips, is a common pest of onions, its role as a vector of P. ananatis has been unknown. The bacterium, P. agglomerans, is also associated with the center rot of onion, but its transmission by thrips has not been previously investigated. In this study, we investigated the relationship of T. tabaci with P. ananatis and P. agglomerans. Surface-sterilized T. tabaci were provided with various acquisition access periods (AAP) on onion leaves inoculated with either P. ananatis or P. agglomerans. A positive exponential relationship was observed between thrips AAP duration and P. ananatis (R2 = 0.967; P = 0.023) or P. agglomerans acquisition (R2 = 0.958; P = 0.017). Transmission experiments conducted with T. tabaci adults indicated that 70% of the seedlings developed center rot symptoms 15 days after inoculation. Immunofluorescence microscopy with antibodies specific to P. ananatis revealed that the bacterium was localized only in the gut of T. tabaci adults. Mechanical inoculation of onion seedlings with fecal rinsates alone produced center rot but not with salivary secretions. Together these results suggested that T. tabaci could efficiently transmit P. ananatis and P. agglomerans.
VerticilliumSystematics and Evolution: How Confusion Impedes Verticillium Wilt Management and How to Resolve It
Authors: Inderbitzin Patrik , Subbarao Krishna V.
Published: February 2014

Verticillium wilts are important vascular wilt diseases that affect many crops and ornamentals in different regions of the world. Verticillium wilts are caused by members of the ascomycete genus Verticillium, a small group of 10 species that are related to the agents of anthracnose caused by Colletotrichum species. Verticillium has a long and complicated taxonomic history with controversies about species boundaries and long overlooked cryptic species, which confused and limited our knowledge of the biology of individual species. We first review the taxonomic history of Verticillium, provide an update and explanation of the current system of classification and compile host range and geographic distribution data for individual species from internal transcribed spacer (ITS) GenBank records. Using Verticillium as an example, we show that species names are a poor vehicle for archiving and retrieving information, and that species identifications should always be backed up by DNA sequence data and DNA extracts that are made publicly available. If such a system were made a prerequisite for publication, all species identifications could be evaluated retroactively, and our knowledge of the biology of individual species would be immune from taxonomic changes, controversy and misidentification. Adoption of this system would improve quarantine practices and the management of diseases caused by various plant pathogens.
Resistance in Mango Against Infection by Ceratocystis fimbriata
Authors: Araujo Leonardo , Bispo Wilka Messner Silva , Cacique Isaías Severino , Moreira Wiler Ribas , Rodrigues Fabrício Ávila
Published: February 2014

This study was designed to characterize and describe host cell responses of stem tissue to mango wilt disease caused by the fungus Ceratocystis fimbriata in Brazil. Disease progress was followed, through time, in inoculated stems for two cultivars, ‘Ubá’ (field resistant) and ‘Haden’ (field susceptible). Stem sections from inoculated areas were examined using fluorescence light microscopy and transmission and scanning electron microscopy, coupled with energy-dispersive X-ray microanalysis. Tissues from Ubá colonized by C. fimbriata had stronger autofluorescence than those from Haden. The X-ray microanalysis revealed that the tissues of Ubá had higher levels of insoluble sulfur and calcium than those of Haden. Scanning electron microscopy revealed that fungal hyphae, chlamydospores (aleurioconidia), and perithecia-like structures of C. fimbriata were more abundant in Haden relative to Ubá. At the ultrastructural level, pathogen hyphae had grown into the degraded walls of parenchyma, fiber cells, and xylem vessels in the tissue of Haden. However, in Ubá, plant cell walls were rarely degraded and hyphae were often surrounded by dense, amorphous granular materials and hyphae appeared to have died. Taken together, the results of this study characterize the susceptible and resistant basal cell responses of mango stem tissue to infection by C. fimbriata.
Geographical variation of human gut microbial composition
Authors: Suzuki Taichi A. , Worobey Michael
Published: February 2014

Although we know there is considerable variation in gut microbial composition within host species, little is known about how this variation is shaped and why such variation exists. In humans, obesity is associated with the relative abundance of two dominant bacterial phyla: an increase in the proportion of Firmicutes and a decrease in the proportion of Bacteroidetes. As there is evidence that humans have adapted to colder climates by increasing their body mass (e.g. Bergmann's rule), we tested whether Firmicutes increase and Bacteroidetes decrease with latitude, using 1020 healthy individuals drawn from 23 populations and six published studies. We found a positive correlation between Firmicutes and latitude and a negative correlation between Bacteroidetes and latitude. The overall pattern appears robust to sex, age and bacterial detection methods. Comparisons between African Americans and native Africans and between European Americans and native Europeans suggest no evidence of host genotype explaining the observed patterns. The variation of gut microbial composition described here is consistent with the pattern expected by Bergmann's rule. This surprising link between large-scale geography and human gut microbial composition merits further investigation.
Management-driven evolution in a domesticated ecosystem
Authors: Vandvik Vigdis , Töpper Joachim P. , Cook Zoë , Daws Matthew I. , Heegaard Einar , Måren Inger E. , Velle Liv Guri
Published: February 2014

Millennia of human land-use have resulted in the widespread occurrence of what have been coined ‘domesticated ecosystems’. The anthropogenic imprints on diversity, composition, structure and functioning of such systems are well documented. However, evolutionary consequences of human activities in these ecosystems are enigmatic.Calluna vulgaris(L.) is a keystone species of coastal heathlands in northwest Europe, an ancient semi-natural landscape of considerable conservation interest. Like many species from naturally fire-prone ecosystems,Callunashows smoke-adapted germination, but it is unclear whether this trait arose prior to the development of these semi-natural landscapes or is an evolutionary response to the anthropogenic fire regime. We show that smoke-induced germination inCallunais found in populations from traditionally burnt coastal heathlands but is lacking in naturally occurring populations from other habitats with infrequent natural fires. Our study thus demonstrates evolutionary imprints of human land-use in semi-natural ecosystems. Evolutionary consequences of historic anthropogenic impacts on wildlife have been understudied, but understanding these consequences is necessary for informed conservation and ecosystem management.
Closing yield gaps: perils and possibilities for biodiversity conservation
Authors: Phalan Ben , Green Rhys , Balmford Andrew
Published: February 2014

Increasing agricultural productivity to ‘close yield gaps’ creates both perils and possibilities for biodiversity conservation. Yield increases often have negative impacts on species within farmland, but at the same time could potentially make it more feasible to minimize further cropland expansion into natural habitats. We combine global data on yield gaps, projected future production of maize, rice and wheat, the distributions of birds and their estimated sensitivity to changes in crop yields to map where it might be most beneficial for bird conservation to close yield gaps as part of a land-sparing strategy, and where doing so might be most damaging. Closing yield gaps to attainable levels to meet projected demand in 2050 could potentially help spare an area equivalent to that of the Indian subcontinent. Increasing yields this much on existing farmland would inevitably reduce its biodiversity, and therefore we advocate efforts both to constrain further increases in global food demand, and to identify the least harmful ways of increasing yields. The land-sparing potential of closing yield gaps will not be realized without specific mechanisms to link yield increases to habitat protection (and restoration), and therefore we suggest that conservationists, farmers, crop scientists and policy-makers collaborate to explore promising mechanisms.
Food security in a perfect storm: using the ecosystem services framework to increase understanding
Authors: Poppy G. M. , Chiotha S. , Eigenbrod F. , Harvey C. A. , Honzák M. , Hudson M. D. , Jarvis A. , Madise N. J. , Schreckenberg K. , Shackleton C. M. , Villa F. , Dawson T. P.
Published: February 2014

Achieving food security in a ‘perfect storm’ scenario is a grand challenge for society. Climate change and an expanding global population act in concert to make global food security even more complex and demanding. As achieving food security and the millennium development goal (MDG) to eradicate hunger influences the attainment of other MDGs, it is imperative that we offer solutions which are complementary and do not oppose one another. Sustainable intensification of agriculture has been proposed as a way to address hunger while also minimizing further environmental impact. However, the desire to raise productivity and yields has historically led to a degraded environment, reduced biodiversity and a reduction in ecosystem services (ES), with the greatest impacts affecting the poor. This paper proposes that the ES framework coupled with a policy response framework, for example Driver-Pressure-State-Impact-Response (DPSIR), can allow food security to be delivered alongside healthy ecosystems, which provide many other valuable services to humankind. Too often, agro-ecosystems have been considered as separate from other natural ecosystems and insufficient attention has been paid to the way in which services can flow to and from the agro-ecosystem to surrounding ecosystems. Highlighting recent research in a large multi-disciplinary project (ASSETS), we illustrate the ES approach to food security using a case study from the Zomba district of Malawi.
Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field
Authors: Qiu Yan-Ling , Kuang Xiao-zhu , Shi Xiao-shuang , Yuan Xian-zheng , Guo Rong-bo
Published: February 2014

A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S
partobacteria’, subdivision 2 of the bacterial phylum

Verrucomicrobia

. Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).
A Novel Approach for Multi-Domain and Multi-Gene Family Identification Provides Insights into Evolutionary Dynamics of Disease Resistance Genes in Core Eudicot Plants
Authors: Hofberger Johannes A. , Zhou Beifei , Tang Haibao , Jones Jonathan D. G. , Schranz M. Eric
Published: February 2014

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity. To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363NB-LRRgenes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection acting on all identified genes and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140NB-LRRgenes present in the model plantArabidopsisand describe four distinct clusters ofNB-LRR“gatekeeper” loci sharing syntelogs across all analyzed genomes. In summary, we designed and implemented an easy-to-follow computational framework for super-gene family identification, and provide the most curated set ofNB-LRRgenes whose genetic versatility among twelve lineages can underpin crop improvement.
A workflow for UPLC-MS non-targeted metabolomic profiling in large human population-based studies
Authors: Ganna Andrea , Fall Tove , Lee Woojoo , Broeckling Corey D. , Kumar Jitender , Hägg Sara , Magnusson Patrik K. E. , Prenni Jessica , Lind Lars , Pawitan Yudi , Ingelsson Erik
Published: February 2014

Metabolomic profiling is an emerging technique in life sciences. Human studies using these techniques have been performed in a small number of individuals or have been targeted at a restricted number of metabolites. In this article, we propose a data analysis workflow to perform non-targeted metabolomic profiling in large human population-based studies using ultra performance liquid chromatography-mass spectrometry (UPLC-MS). We describe challenges and propose solutions for quality control, statistical analysis and annotation of metabolic features. Using the data analysis workflow, we detected more than 8,000 metabolic features in serum samples from 2,489 fasting individuals. As an illustrative example, we performed a non-targeted metabolome-wide association analysis of high-sensitive C-reactive protein (hsCRP) and detected 407 metabolic features corresponding to 90 unique metabolites that could be replicated in an external population. Our results reveal unexpected biological associations, such as metabolites identified as monoacylphosphorylcholines (LysoPC) being negatively associated with hsCRP. R code and fragmentation spectra for all metabolites are made publically available. In conclusion, the results presented here illustrate the viability and potential of non-targeted metabolomic profiling in large population-based studies.
Ethyl 3-(9-chloro-10-oxo-9,10-dihydroanthracen-9-yl)-5-methylisoxazole-4-carboxylate
Authors: Duncan Nathan S. , Beall Howard D. , Kearns Alison K. , Li Chun , Natale Nicholas R.
Published: February 2014

The asymmetric unit of the title compound, C21H16ClNO4, contains two independent molecules (AandB), each adopting a conformation wherein the isoxazole ring is roughly orthogonal to the anthrone ring. The dihedral angle between the mean plane of the isoxazole (all atoms) and the mean plane of the anthrone (all atoms) is 88.48 (3)° in one molecule and 89.92 (4)° in the other. The ester is almost coplanar with the isoxazole ring, with mean-plane dihedral angles of 2.48 (15) and 8.62 (5)°. In both molecules, the distance between the ester carbonyl O atom and the anthrone ketone C atom is about 3.3 Å. The anthrone ring is virtually planar (r.m.s. deviations of 0.070 and 0.065 Å) and adopts a shallow boat conformation in each molecule, as evidenced by the sum of the six intra-B-ring torsion angles [41.43 (15) and 34.38 (15)° for moleculesAandB, respectively]. The closest separation between the benzene moieties of anthronesAandBis 5.1162 (7) Å, with an angle of 57.98 (5)°, consistent with an edge-to-face π-stacking interaction. In the crystal, weak C—H...O and C—H...N interactions link the molecules, forming a three-dimensional network.
Twinned caesium cerium(IV) pentafluoride
Authors: Grzechnik Andrzej , Underwood Christopher C. , Kolis Joseph W.
Published: February 2014

Single-crystals of CsCeF5were synthesized hydrothermally. The crystal under investigation was twinned by pseudo-merohedry with a twofold rotation around thecaxis as an additional twinning operation. The crystal structure is built of layers of distorted edge- and corner-sharing CeF8square-antiprisms. The Cs+cations are located between the layers and exhibit coordination numbers of nine. Upon compression, CsCeF5undergoes an irreversible phase transition at about 1 GPa.
Heterogeneous hosts: how variation in host size, behaviour and immunity affects parasite aggregation
Authors: Johnson Pieter T. J. , Hoverman Jason T.
Published: February 2014

Infection heterogeneity is one of the most fundamental patterns in disease ecology, yet surprisingly few studies have experimentally explored its underlying drivers. Here, we used large‐scale field assessments to evaluate the degree of parasite aggregation within amphibian host populations followed by a novel experimental approach to assess the potential influence of host size, behaviour and immunity in reproducing such heterogeneity.

Among 227 wetlands, 2468 hosts and seven parasite species, infections were consistently aggregated among host individuals within populations of the Pacific chorus frog (Pseudacris regilla). For each parasite species, the relationship between the log‐mean and log‐variance of infection load was strongly linear (R2: 0·91–0·98) with a slope between 1·37 and 1·67, indicative of aggregation relative to the expected Poisson slope of unity.

In laboratory trials withP. regillaand the most virulent trematode (Ribeiroia ondatrae), experimental reductions in either host immunity (through corticosterone exposure) or antiparasite behaviours (through anaesthesia exposure) increased parasite infection loads in isolated hosts by 62–102% relative to unmanipulated individuals. In a second experiment designed to test how variation in host immunity, behaviour and body size affected variation in infection load within small groups (dyads), a reduction in immune function or behaviour of one host significantly amplified infection heterogeneity within the group, effectively doubling the variance‐to‐mean ratio. However, immunity affected aggregation only in the absence of behavioural manipulation, and changing the size distribution of hosts did not appreciably affect aggregation.

Using Taylor's Power Law to integrate field and laboratory data, we found that only treatments involving behavioural reductions achieved aggregation levels comparable to natural host populations. Thus, despite their short duration, our treatments generated heterogeneity in infection loads similar to natural observations.

These results emphasize how, alongside extrinsic variation in parasite exposure risk, individual host attributes generally and behaviour in particular have the potential to influence infection success and parasite aggregation. Continued integration of infection heterogeneity research across space, among host species, and over time has important implications for understanding and managing human and wildlife diseases.
Effects of prey metapopulation structure on the viability of black‐footed ferrets in plague‐impacted landscapes: a metamodelling approach
Authors: Shoemaker Kevin T. , Lacy Robert C. , Verant Michelle L. , Brook Barry W. , Livieri Travis M. , Miller Philip S. , Fordham Damien A. , Resit Akçakaya H.
Published: February 2014

Species interactions have been largely ignored in extinction risk assessment. However, the black‐footed ferret Mustela nigripes exemplifies a class of endangered species for which strong species interactions cannot be ignored. This species is an obligate predator of prairie dogs Cynomys spp., and sylvatic plague Yersinia pestis epizootics threaten to undermine recovery efforts by functionally eliminating the prey base. Multispecies ‘metamodelling’ techniques offer new opportunities for exploring population dynamics under strong species interdependencies and disease.

To investigate ferret extinction risk in plague‐affected landscapes, we simultaneously modelled plague epidemiological processes, prairie dog metapopulation dynamics and ferret demographic responses. Ferret population dynamics were investigated at an important release site (Conata Basin in South Dakota) and for 500 artificial prey landscapes spanning a wide range of realistic colony configurations (e.g. total area, # colonies, spatial clustering) and demographic characteristics.

Our simulation models indicate that ferrets are unlikely to persist through episodes of plague at Conata Basin unless they can access prey resources from a wider region or unless management actions can otherwise substantially reduce plague transmission.

We show that large, diffuse prairie dog metapopulations (those with colonies spread over a region >2500 km2) are most likely to support ferret populations in plague‐affected landscapes. Our results also highlight the potential importance of metapopulation connectivity in fuelling plague epizootics and thereby imperilling black‐footed ferret conservation efforts.

We describe a cycle (c. 5‐ to 25‐year period) of plague‐driven population crashes that is an emergent property of our models, and which can destabilize ferret populations.

Synthesis and applications. On the basis of our models, we conclude that few North American prairie dog complexes cover sufficient land area to sustain black‐footed ferret populations through plague‐driven crashes in prey abundance. Consequently, our results underscore the importance of working with many constituents to conserve large prairie dog landscapes in addition to continued development of plague mitigation tools. In addition, the strong relationship between plague‐induced oscillatory prey cycles and predator population persistence highlights the potential conservation benefits of imposing strategic barriers to connectivity in areas over which plague outbreak cycles are strongly synchronous.
Urbanizing Urban Political Ecology: A Critique of Methodological Cityism
Authors: Angelo Hillary , Wachsmuth David
Published: February 2014

Urban political ecology (UPE), an offshoot of political ecology that emerged in the late 1990s, has had two major impacts on critical urban studies: it has introduced critical political ecology to urban settings, and it has provided a framework for retheorizing the city as a product of metabolic processes of socionatural transformation. However, there was another goal in early UPE programmatic statements that has largely fallen by the wayside: to mobilize a Lefebvrian theoretical framework to trouble traditional distinctions between urban/rural and society/nature by exploring urbanization as a global process. Instead of following this potentially fruitful path, UPE has become bogged down in ‘methodological cityism’––an overwhelming analytical and empirical focus on the traditional city to the exclusion of other aspects of contemporary urbanization processes. Thus UPE's Lefebvrian promise, of a research program that could work across traditional disciplinary divisions and provide insights into a new era of planetary urbanization, has remained unfulfilled. In this article we trace UPE's history to show how it arrived at its present predicament, and offer some thoughts on a research agenda for a political ecology not of the city but of urbanization.
Heterosis in age‐specific selected populations of a seed beetle: Sex differences in longevity and reproductive behavior
Authors: Stojković Biljana , Đorđević Mirko , Janković Jelena , Savković Uroš , Tucić Nikola
Published: February 2014

We tested mutation accumulation hypothesis for the evolution of senescence using short‐lived and long‐lived populations of the seed‐feeding beetle, Acanthoscelides obtectus (Say), obtained by selection on early‐ and late‐life for many generations. The expected consequence of the mutation accumulation hypothesis is that in short‐lived populations, where the force of natural selection is the strongest early in life, the late‐life fitness traits should decline due to genetic drift which increases the frequency of mutations with deleterious effects in later adult stages. Since it is unlikely that identical deleterious mutations will increase in several independent populations, hybrid vigor for late‐life fitness is expected in offspring obtained in crosses among populations selected for early‐life fitness traits. We tested longevity of both sexes, female fecundity and male reproductive behavior for hybrid vigor by comparing hybrid and nonhybrid short‐lived populations. Hybrid vigor was confirmed for male virility, mating speed and copulation duration, and longevity of both sexes at late ages. In contrast to males, the results on female fecundity in short‐lived populations did not support mutation accumulation as a genetic mechanism for the evolution of this trait. Contrary to the prediction of this hypothesis, male mating ability indices and female fecundity in long‐lived populations exhibited hybrid vigor at all assayed age classes. We demonstrate that nonhybrid long‐lived populations diverged randomly regarding female and male reproductive fitness, indicating that sexually antagonistic selection, when accompanied with genetic drift for female fecundity and male virility, might be responsible for overriding natural selection in the independently evolving long‐lived populations.
Flexible work arrangements, work engagement, turnover intentions and psychological health
Authors: Timms Carolyn , Brough Paula , O'Driscoll Michael , Kalliath Thomas , Siu Oi Ling , Sit Cindy , Lo Danny
Published: February 2014

Flexible work arrangements (FWAs) are often written into company policies to demonstrate organisational sensitivity to potentially difficult interfaces between employees' work and non‐work domains. The current research investigated employees' use of FWAs and relationship to work engagement, with turnover intentions and psychological strain also used as criterion variables for comparison purposes. A heterogeneous sample of Australian employees (N = 823) responded to two waves of data collection separated by a 12‐month interval. It was expected that supportive aspects of organisational culture would be consistent with increased employee utilisation of FWAs, high work engagement, low turnover and low levels of psychological strain, and the opposite would be found for hindering aspects of organisational culture. It was also expected that supportive organisational culture would demonstrate an enduring effect over time. In general, research findings supported these hypotheses. However, the research also identified a negative relationship between use of FWAs and work engagement over time. This suggests that take‐up of FWAs is highly dependent on workplace cultural norms. The implications of these results are discussed.
Antioxidant and Anti‐inflammatory Activities of Methanol Extracts of Tremella fuciformis and Its Major Phenolic Acids
Authors: Li Hua , Lee Hee‐Seok , Kim Su‐Hwan , Moon BoKyung , Lee Chan
Published: February 2014

Methanol extract subfractions of the edible white jelly mushroom (Tremella fuciformis), were assessed for the following antioxidant properties: ABTS+ radical scavenging activity, 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) radical scavenging activity, and inhibitory activity of human low‐density lipoprotein (LDL) oxidation. Among the subfractions tested, the chloroform subfraction exhibited the strongest antioxidant activity, with the highest total phenolic content (66.31 μg CAE/mg extract) and flavonoids content (5.12 μg QE/mg extract). The ABTS+ radical scavenging activity of the chloroform subfraction was 7.89 μmol trolox/mg extract, which was the highest among all subfractions. This subfraction also showed the highest DPPH radical scavenging activity and inhibitory activity of LDL oxidation. In addition, the chloroform subfraction demonstrated anti‐inflammatory activity through inhibition of nitric oxide production and inducible nitric oxide synthase expression in RAW 264.7 cells. Major phenolic acids from the mushroom extract were identified as 4‐hydroxybenzoic acid (323 mg/kg dry weight of mushroom), gentisic acid (174 mg/kg dry weight of mushroom), and 4‐coumaric acid (30 mg/kg dry weight of mushroom).
Tracking dietary habits of cave arthropods associated with deposits of hematophagous bat guano: A study from a neotropical savanna
Authors: Salgado Simone S. , Motta Paulo C. , de Souza Aguiar Ludmilla M. , Nardoto Gabriela B.
Published: February 2014

Carbon and nitrogen stable isotopes were used to track major dietary variations in arthropods found in a cave located in a neotropical savanna in Central Brazil. We determined the δ13C and δ15N for cave crickets, cockroaches, spiders, guano of a hematophagous bat, and leaf litter found on the ground near the cave entrance. The δ13C and δ15N for the cricket and cockroaches showed that bat guano was not the only food item for these arthropods. They had intermediate δ13C and δ15N between bat guano and leaf litter, which means that they consumed additional food resources other than guano in their diet, independent of distribution of guano deposits in the cave. The spiders, predators with great mobility, seemed to not have a preferential diet item since their isotope signals indicated they hunt both crickets and cockroaches. The δ13C of the bat guano (−15.4‰) indicated that the diet of these hematophagous bats relied on animals fed with C4 plants. The conversion of native savanna vegetation of which the debris is mostly from C3 plants, to pasture, based on C4 African grass, a remarkably common land use transformation in the region, is indirectly influencing the diet of hematophagous bats, which basically relied on exotic fauna. The C and N stable isotope ratios showed that the arthropods inside the cave do not rely solely on bat guano for their diet, but interact directly with the external environment, through litter debris, indicating a significant exchange of energy and matter between the cave environment and the surrounding area.
Validation of a landscape‐scale planning tool for cavity‐dependent wildlife
Authors: Stojanovic Dejan , Koch Amelia J. , Webb Matthew , Cunningham Ross , Roshier David , Heinsohn Robert
Published: February 2014

Tree cavities provide important habitat for wildlife. Effective landscape‐scale management of cavity‐dependent wildlife requires an understanding of where cavities occur, but tree cavities can be cryptic and difficult to survey. We assessed whether a landscape‐scale map of mature forest habitat availability, derived from aerial photographs, reflected the relative availability of mature trees and tree cavities. We assessed cavities for their suitability for use by wildlife, and whether the map reflected the availability of such cavities. There were significant differences between map categories in several characteristics of mature trees that can be used to predict cavity abundance (i.e. tree form and diameter at breast height). There were significant differences between map categories in the number of potential cavity bearing trees and potential cavities per tree. However, the index of cavity abundance based on observations made from the ground provided an overestimate of true cavity availability. By climbing a sample of mature trees we showed that only 5.1% of potential tree cavities detected from the ground were suitable for wildlife, and these were found in only 12.5% of the trees sampled. We conclude that management tools developed from remotely sensed data can be useful to guide decision‐making in the conservation management of tree cavities but stress that the errors inherent in these data limit the scale at which such tools can be applied. The rarity of tree cavities suitable for wildlife in our study highlights the need to conserve the tree cavity resource across the landscape, but also the importance of increasing the accuracy of management tools for decision‐making at different scales. Mapping mature forest habitat availability at the landscape scale is a useful first step in managing habitat for cavity‐dependent wildlife, but the potential for overestimating actual cavity abundance in a particular area highlights the need for complementary on‐ground surveys.