bluuebunny/crossref_metadata_2025 huggingface dataset:
BEYOND TOCQUEVILLE: A PLEA TO STOP “TAKING RELIGION SERIOUSLY”
Authors: CHAPPEL JAMES
Published: October 2013

We have all heard the admonition to “take religion seriously.” It is a perplexing command, since AHA statistics indicate that graduate students have been flocking to religious topics for years. Library shelves groan under the weight of recent works that take religion seriously. What, then, might it mean to take religion more seriously, as it has been such a booming academic field for decades now? As Elizabeth Pritchard has pointed out, the imperative is not a methodological recommendation at all, but an ethical–political one. To take religion “seriously” is to grant it its rightful place as an independent variable amidst others, without reducing it to the old categories of politics or class or gender. It is implicitly frivolous to see religion as a superstructural manifestation of a deeper social or economic reality, as have many functionalist theories from Marx onwards. These accounts are routinely pilloried as condescending towards the past, and as failing to take historical actors at their word when they claim to act for religious reasons. There is much to this; nonetheless, the currently reigning assumption of religious autonomy, like that of other cultural artifacts, has been perilously undertheorized. In this joint review, I would like to show how this understanding of religion impedes historical understanding. It might be the case that, to paraphrase Oscar Wilde, religion is too important to take seriously.
Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes
Authors: Kinkel Linda L , Schlatter Daniel C , Xiao Kun , Baines Anita D
Published: October 2013

Soil bacteria produce a diverse array of antibiotics, yet our understanding of the specific roles of antibiotics in the ecological and evolutionary dynamics of microbial interactions in natural habitats remains limited. Here, we show a significant role for antibiotics in mediating antagonistic interactions and nutrient competition among locally coexisting Streptomycete populations from soil. We found that antibiotic inhibition is significantly more intense among sympatric than allopatric Streptomycete populations, indicating local selection for inhibitory phenotypes. For sympatric but not allopatric populations, antibiotic inhibition is significantly positively correlated with niche overlap, indicating that inhibition is targeted toward bacteria that pose the greatest competitive threat. Our results support the hypothesis that antibiotics serve as weapons in mediating local microbial interactions in soil and suggest that coevolutionary niche displacement may reduce the likelihood of an antibiotic arms race. Further insight into the diverse roles of antibiotics in microbial ecology and evolution has significant implications for understanding the persistence of antibiotic inhibitory and resistance phenotypes in environmental microbes, optimizing antibiotic drug discovery and developing strategies for managing microbial coevolutionary dynamics to enhance inhibitory phenotypes.
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
Authors: Embree Mallory , Nagarajan Harish , Movahedi Narjes , Chitsaz Hamidreza , Zengler Karsten
Published: October 2013

Microbial interactions have a key role in global geochemical cycles. Although we possess significant knowledge about the general biochemical processes occurring in microbial communities, we are often unable to decipher key functions of individual microorganisms within the environment in part owing to the inability to cultivate or study them in isolation. Here, we circumvent this shortcoming through the use of single-cell genome sequencing and a novel low-input metatranscriptomics protocol to reveal the intricate metabolic capabilities and microbial interactions of an alkane-degrading methanogenic community. This methanogenic consortium oxidizes saturated hydrocarbons under anoxic conditions through a thus-far-uncharacterized biochemical process. The genome sequence of a dominant bacterial member of this community, belonging to the genus Smithella, was sequenced and served as the basis for subsequent analysis through metabolic reconstruction. Metatranscriptomic data generated from less than 500 pg of mRNA highlighted metabolically active genes during anaerobic alkane oxidation in comparison with growth on fatty acids. These data sets suggest that Smithella is not activating hexadecane by fumarate addition. Differential expression assisted in the identification of hypothetical proteins with no known homology that may be involved in hexadecane activation. Additionally, the combination of 16S rDNA sequence and metatranscriptomic data enabled the study of other prevalent organisms within the consortium and their interactions with Smithella, thus yielding a comprehensive characterization of individual constituents at the genome scale during methanogenic alkane oxidation.
Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool
Authors: Stalder Thibault , Barraud Olivier , Jové Thomas , Casellas Magali , Gaschet Margaux , Dagot Christophe , Ploy Marie- Cécile
Published: October 2013

There is increasing evidence that human activity, and especially the resulting effluent, has a major role in the dissemination of bacterial antibiotic-resistance determinants in the environment. Hospitals are the major antibiotic consumers and thus facilitate the spread of antibiotic resistance. Questions are increasingly being raised about the management of hospital effluents, but their involvement in antibiotic-resistance dissemination has never been assessed. Integrons are a paradigm of genetic transfer between the environmental resistome and both commensal and pathogenic bacteria. In order to assess the impact of hospital activities on antibiotic-resistance dissemination in the environment, we monitored integrons and their gene cassettes in hospital effluents, and their release in the environment. We found that bacterial communities present in a hospital effluent contained a high proportion of integrons. In terms of both their gene cassette diversity and gene cassette arrays, the urban effluent and municipal wastewater treatment plant (WWTP) influent were most similar, whereas the hospital effluent and recirculation sludge exhibited very specific patterns. We found that anthropogenic activities led to the release of abundant integrons and antibiotic-resistance gene cassettes, but we observed no specific impact of hospital activities on the receiving environment. Furthermore, although the WWTP did not reduce the normalized integron copy number, it reduced the diversity of gene cassette arrays contained in the raw wastewater, underlining the effect of the biological treatment on the anthropogenic integron pool arriving at the WWTP.
Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes
Authors: Vick-Majors Trista J , Priscu John C , Amaral-Zettler Linda A
Published: October 2013

High-latitude environments, such as the Antarctic McMurdo Dry Valley lakes, are subject to seasonally segregated light–dark cycles, which have important consequences for microbial diversity and function on an annual basis. Owing largely to the logistical difficulties of sampling polar environments during the darkness of winter, little is known about planktonic microbial community responses to the cessation of photosynthetic primary production during the austral sunset, which lingers from approximately February to April. Here, we hypothesized that changes in bacterial, archaeal and eukaryotic community structure, particularly shifts in favor of chemolithotrophs and mixotrophs, would manifest during the transition to polar night. Our work represents the first concurrent molecular characterization, using 454 pyrosequencing of hypervariable regions of the small-subunit ribosomal RNA gene, of bacterial, archaeal and eukaryotic communities in permanently ice-covered lakes Fryxell and Bonney, before and during the polar night transition. We found vertically stratified populations that varied at the community and/or operational taxonomic unit-level between lakes and seasons. Network analysis based on operational taxonomic unit level interactions revealed nonrandomly structured microbial communities organized into modules (groups of taxa) containing key metabolic potential capacities, including photoheterotrophy, mixotrophy and chemolithotrophy, which are likely to be differentially favored during the transition to polar night.
Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress
Authors: Darby Alistair C , Gill A Christina , Armstrong Stuart D , Hartley Catherine S , Xia Dong , Wastling Jonathan M , Makepeace Benjamin L
Published: October 2013

The bacterium Wolbachia (order Rickettsiales), representing perhaps the most abundant vertically transmitted microbe worldwide, infects arthropods and filarial nematodes. In arthropods, Wolbachia can induce reproductive alterations and interfere with the transmission of several arthropod-borne pathogens. In addition, Wolbachia is an obligate mutualist of the filarial parasites that cause lymphatic filariasis and onchocerciasis in the tropics. Targeting Wolbachia with tetracycline antibiotics leads to sterilisation and ultimately death of adult filariae. However, several weeks of treatment are required, restricting the implementation of this control strategy. To date, the response of Wolbachia to stress has not been investigated, and almost nothing is known about global regulation of gene expression in this organism. We exposed an arthropod Wolbachia strain to doxycycline in vitro, and analysed differential expression by directional RNA-seq and label-free, quantitative proteomics. We found that Wolbachia responded not only by modulating expression of the translation machinery, but also by upregulating nucleotide synthesis and energy metabolism, while downregulating outer membrane proteins. Moreover, Wolbachia increased the expression of a key component of the twin-arginine translocase (tatA) and a phosphate ABC transporter ATPase (PstB); the latter is associated with decreased susceptibility to antimicrobials in free-living bacteria. Finally, the downregulation of 6S RNA during translational inhibition suggests that this small RNA is involved in growth rate control. Despite its highly reduced genome, Wolbachia shows a surprising ability to regulate gene expression during exposure to a potent stressor. Our findings have general relevance for the chemotherapy of obligate intracellular bacteria and the mechanistic basis of persistence in the Rickettsiales.
Base excision repair AP endonucleases and mismatch repair act together to induce checkpoint-mediated autophagy
Authors: SenGupta Tanima , Torgersen Maria Lyngaas , Kassahun Henok , Vellai Tibor , Simonsen Anne , Nilsen Hilde
Published: October 2013

Cellular responses to DNA damage involve distinct DNA repair pathways, such as mismatch repair (MMR) and base excision repair (BER). UsingCaenorhabditis elegansas a model system, we present genetic and molecular evidence of a mechanistic link between processing of DNA damage and activation of autophagy. Here we show that the BER AP endonucleases APN-1 and EXO-3 function in the same pathway as MMR, to elicit DNA-directed toxicity in response to 5-fluorouracil, a mainstay of systemic adjuvant treatment of solid cancers. Immunohistochemical analyses suggest that EXO-3 generates the DNA nicks required for MMR activation. Processing of DNA damage via this pathway, in which both BER and MMR enzymes are required, leads to induction of autophagy inC. elegansand human cells. Hence, our data show that MMR- and AP endonuclease-dependent processing of 5-fluorouracil-induced DNA damage leads to checkpoint activation and induction of autophagy, whose hyperactivation contributes to cell death.
CD72 regulates the growth of KIT-mutated leukemia cell line Kasumi-1
Authors: Kataoka Tatsuki R. , Kumanogoh Atsushi , Hirata Masahiro , Moriyoshi Koki , Ueshima Chiyuki , Kawahara Masahiro , Tsuruyama Tatsuaki , Haga Hironori
Published: October 2013

Gain-of-function mutations in KIT, a member of the receptor type tyrosine kinases, are observed in certain neoplasms, including mast cell tumors (MCTs) and acute myelogenous leukemias (AMLs). A MCT line HMC1.2 harboring the KIT mutation was reported to express CD72, which could suppress the cell proliferation. Here, we examined the ability of CD72 to modify the growth of AMLs harboring gain-of-function KIT mutations. CD72 was expressed on the surface of the AML cell line, Kasumi-1. CD72 ligation by an agonistic antibody BU40 or by a natural ligand CD100, suppressed the proliferation of the Kasumi-1 cells and enhanced cell death, as monitored by caspase-3 cleavage. These responses were associated with the phosphorylation of CD72, the formation of the CD72 - SHP-1 complex and dephosphorylation of src family kinases and JNK. Thus, these results seemed to suggest that CD72 was the therapeutic potential for AML, as is the case of MCTs.
Cellular network entropy as the energy potential in Waddington's differentiation landscape
Authors: Banerji Christopher R. S. , Miranda-Saavedra Diego , Severini Simone , Widschwendter Martin , Enver Tariq , Zhou Joseph X. , Teschendorff Andrew E.
Published: October 2013

Differentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark of a cellular sample's position in the global differentiation hierarchy. Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile. We demonstrate that network entropy provides a quantitative, in-silico, readout of the average undifferentiated state of the profiled cells, recapitulating the known hierarchy of pluripotent, multipotent and differentiated cell types. Network entropy further exhibits dynamic changes in time course differentiation data, and in line with a sample's differentiation stage. In disease, network entropy predicts a higher level of cellular plasticity in cancer stem cell populations compared to ordinary cancer cells. Importantly, network entropy also allows identification of key differentiation pathways. Our results are consistent with the view that pluripotency is a statistical property defined at the cellular population level, correlating with intra-sample heterogeneity, and driven by the degree of signaling promiscuity in cells. In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape.
Analysis of the Sam50 translocase of Excavate organisms supports evolution of divergent organelles from a common endosymbiotic event
Authors: Kay Christopher J. , Lawler Karen , Kerr Ian D.
Published: October 2013

As free-living organisms the ancestors of mitochondria and plastids encoded complete genomes, proteomes and metabolomes. As these symbionts became organelles all these aspects were reduced – genomes have degenerated with the host nucleus now encoding the most of the remaining endosymbiont proteome, while the metabolic processes of the symbiont have been streamlined to the functions of the emerging organelle. By contrast, the topology of the endosymbiont membrane has been preserved, necessitating the development of complex pathways for membrane insertion and translocation. In this study, we examine the characteristics of the endosymbiont-derived β-barrel insertase Sam501 in the excavate super-group. A candidate is further characterized in Trichomonas vaginalis, an unusual eukaryote possessing degenerate hydrogen-producing mitochondria called hydrogenosomes. This information supports a mitochondriate eukaryotic common ancestor with a similarly evolved β-barrel insertase, which has continued to be conserved in degenerate mitochondria.
Mouse model of intrahepatic cholangiocarcinoma validates FIG–ROS as a potent fusion oncogene and therapeutic target
Authors: Saborowski Anna , Saborowski Michael , Davare Monika A. , Druker Brian J. , Klimstra David S. , Lowe Scott W.
Published: October 2013

Significance

Intrahepatic cholangiocarcinoma (ICC) is a fatal yet understudied primary liver malignancy. To accelerate the functional annotation of cancer genes and therapeutic targets in this disease, we generate a highly flexible orthotopic allograft mouse model of ICC that can be easily modified in vitro to mimic either oncogene expression by retrovirus-mediated gene transfer or tumor-suppressor gene loss by using RNA interference technology. We use this model to demonstrate that the fused-in-glioblastoma-c-ros-oncogene 1 (
FIG-ROS
) fusion, which is found in a subset of ICC patients, accelerates cholangiocarcinogenesis. Moreover, by using reversible gene expression, we show that FIG–ROS inactivation in carcinomas harboring mutant kirsten rat sarcoma viral oncogene homolog (
Kras
) and
p53
mutations can potently inhibit tumor growth, thereby validating ROS as a therapeutic target in ICC.
Emerin organizes actin flow for nuclear movement and centrosome orientation in migrating fibroblasts
Authors: Chang Wakam , Folker Eric S. , Worman Howard J. , Gundersen Gregg G.
Published: October 2013

In migrating fibroblasts, rearward movement of the nucleus orients the centrosome toward the leading edge. Nuclear movement results from coupling rearward-moving, dorsal actin cables to the nucleus by linear arrays of nesprin-2G and SUN2, termed transmembrane actin-associated nuclear (TAN) lines. A-type lamins anchor TAN lines, prompting us to test whether emerin, a nuclear membrane protein that interacts with lamins and TAN line proteins, contributes to nuclear movement. In fibroblasts depleted of emerin, nuclei moved nondirectionally or completely failed to move. Consistent with these nuclear movement defects, dorsal actin cable flow was nondirectional in cells lacking emerin. TAN lines formed normally in cells lacking emerin and were coordinated with the erratic nuclear movements, although in 20% of the cases, TAN lines slipped over immobile nuclei. Myosin II drives actin flow, and depletion of myosin IIB, but not myosin IIA, showed similar nondirectional nuclear movement and actin flow as in emerin-depleted cells. Myosin IIB specifically coimmunoprecipitated with emerin, and emerin depletion prevented myosin IIB localization near nuclei. These results show that emerin functions with myosin IIB to polarize actin flow and nuclear movement in fibroblasts, suggesting a novel function for the nuclear envelope in organizing directional actin flow and cytoplasmic polarity.
The spatial segregation of pericentric cohesin and condensin in the mitotic spindle
Authors: Stephens Andrew D. , Quammen Cory W. , Chang Binny , Haase Julian , Taylor Russell M. , Bloom Kerry
Published: October 2013

In mitosis, the pericentromere is organized into a spring composed of cohesin, condensin, and a rosette of intramolecular chromatin loops. Cohesin and condensin are enriched in the pericentromere, with spatially distinct patterns of localization. Using model convolution of computer simulations, we deduce the mechanistic consequences of their spatial segregation. Condensin lies proximal to the spindle axis, whereas cohesin is radially displaced from condensin and the interpolar microtubules. The histone deacetylase Sir2 is responsible for the axial position of condensin, while the radial displacement of chromatin loops dictates the position of cohesin. The heterogeneity in distribution of condensin is most accurately modeled by clusters along the spindle axis. In contrast, cohesin is evenly distributed (barrel of 500-nm width × 550-nm length). Models of cohesin gradients that decay from the centromere or sister cohesin axis, as previously suggested, do not match experimental images. The fine structures of cohesin and condensin deduced with subpixel localization accuracy reveal critical features of how these complexes mold pericentric chromatin into a functional spring.
The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome
Authors: Niepel Mario , Molloy Kelly R. , Williams Rosemary , Farr Julia C. , Meinema Anne C. , Vecchietti Nicholas , Cristea Ileana M. , Chait Brian T. , Rout Michael P. , Strambio-De-Castillia Caterina
Published: October 2013

The basket of the nuclear pore complex (NPC) is generally depicted as a discrete structure of eight protein filaments that protrude into the nucleoplasm and converge in a ring distal to the NPC. We show that the yeast proteins Mlp1p and Mlp2p are necessary components of the nuclear basket and that they also embed the NPC within a dynamic protein network, whose extended interactome includes the spindle organizer, silencing factors, the proteasome, and key components of messenger ribonucleoproteins (mRNPs). Ultrastructural observations indicate that the basket reduces chromatin crowding around the central transporter of the NPC and might function as a docking site for mRNP during nuclear export. In addition, we show that the Mlps contribute to NPC positioning, nuclear stability, and nuclear envelope morphology. Our results suggest that the Mlps are multifunctional proteins linking the nuclear transport channel to multiple macromolecular complexes involved in the regulation of gene expression and chromatin maintenance.
Ubiquitination-dependent quality control of hERG K+ channel with acquired and inherited conformational defect at the plasma membrane
Authors: Apaja Pirjo M. , Foo Brian , Okiyoneda Tsukasa , Valinsky William C. , Barriere Herve , Atanasiu Roxana , Ficker Eckhard , Lukacs Gergely L. , Shrier Alvin
Published: October 2013

Membrane trafficking in concert with the peripheral quality control machinery plays a critical role in preserving plasma membrane (PM) protein homeostasis. Unfortunately, the peripheral quality control may also dispose of partially or transiently unfolded polypeptides and thereby contribute to the loss-of-expression phenotype of conformational diseases. Defective functional PM expression of the human ether-a-go-go–related gene (hERG) K+ channel leads to the prolongation of the ventricular action potential that causes long QT syndrome 2 (LQT2), with increased propensity for arrhythmia and sudden cardiac arrest. LQT2 syndrome is attributed to channel biosynthetic processing defects due to mutation, drug-induced misfolding, or direct channel blockade. Here we provide evidence that a peripheral quality control mechanism can contribute to development of the LQT2 syndrome. We show that PM hERG structural and metabolic stability is compromised by the reduction of extracellular or intracellular K+ concentration. Cardiac glycoside–induced intracellular K+ depletion conformationally impairs the complex-glycosylated channel, which provokes chaperone- and C-terminal Hsp70-interacting protein–dependent polyubiquitination, accelerated internalization, and endosomal sorting complex required for transport–dependent lysosomal degradation. A similar mechanism contributes to the down-regulation of PM hERG harboring LQT2 missense mutations, with incomplete secretion defect. These results suggest that PM quality control plays a determining role in the loss-of-expression phenotype of hERG in certain hereditary and acquired LTQ2 syndromes.
Estrogen regulates histone deacetylases to prevent cardiac hypertrophy
Authors: Pedram Ali , Razandi Mahnaz , Narayanan Ramesh , Dalton James T. , McKinsey Timothy A. , Levin Ellis R.
Published: October 2013

The development and progression of cardiac hypertrophy often leads to heart failure and death, and important modulators of hypertrophy include the histone deacetylase proteins (HDACs). Estrogen inhibits cardiac hypertrophy and progression in animal models and humans. We therefore investigated the influence of 17-β-estradiol on the production, localization, and functions of prohypertrophic (class I) and antihypertrophic (class II) HDACs in cultured neonatal rat cardiomyocytes. 17-β-Estradiol or estrogen receptor β agonists dipropylnitrile and β-LGND2 comparably suppressed angiotensin II–induced HDAC2 (class I) production, HDAC-activating phosphorylation, and the resulting prohypertrophic mRNA expression. In contrast, estrogenic compounds derepressed the opposite effects of angiotensin II on the same parameters for HDAC4 and 5 (class II), resulting in retention of these deacetylases in the nucleus to inhibit hypertrophic gene expression. Key aspects were confirmed in vivo from the hearts of wild-type but not estrogen receptor β (ERβ) gene–deleted mice administered angiotensin II and estrogenic compounds. Our results identify a novel dual regulation of cardiomyocyte HDACs, shown here for the antihypertrophic sex steroid acting at ERβ. This mechanism potentially supports using ERβ agonists as HDAC modulators to treat cardiac disease.
From Hopeless to Curious? Thoughts on Hausman's “Dubious to Hopeless” Critique of Contingent Valuation
Authors: Haab Timothy C. , Interis Matthew G. , Petrolia Daniel R. , Whitehead John C.
Published: October 2013

Hausman “selectively” reviewed the contingent valuation method (CVM) literature in 2012 and failed to find progress in the method during the 18 years since Diamond and Hausman argued that unquantified benefits and costs are preferred to those quantified by CVM. In this manuscript, we provide counter‐arguments to Hausman's claims, not with the intent to convince the reader that the debate over CVM is settled in favor of the method, but rather to argue that the intellectual debate over CVM is ongoing, that dismissing CVM is unwarranted, and that plenty of work remains to be done for the truly curious researcher.
Principles of International Investment Law
Authors: Dolzer Rudolf , Schreuer Christoph
Published: October 2013

This book outlines the principles behind the international law of foreign investment, focusing on the law governed by bilateral and multilateral investment treaties. The book traces the purpose, context, and evolution of the clauses and provisions characteristic of contemporary investment treaties, and analyses the case law interpreting the issues raised by standard clauses. Particular consideration is given to broad treaty-rules whose understanding in practice has mainly been shaped by their interpretation and application by international tribunals. In addition, the book introduces the dispute settlement mechanisms for enforcing investment law, outlining the operation of State vs. State and Investor vs. State arbitration. Combining a systematic analytical study of the texts and principles underlying investment law with a jurisprudential analysis of the case law arising in international tribunals, this book introduces the principles of international investment law and arbitration.
Herschel observations and a model for IRAS 08572+3915: a candidate for the most luminous infrared galaxy in the local (
z < 0.2) Universe
Authors: Efstathiou A. , Pearson C. , Farrah D. , Rigopoulou D. , Graciá-Carpio J. , Verma A. , Spoon H. W. W. , Afonso J. , Bernard-Salas J. , Clements D. L. , Cooray A. , Cormier D. , Etxaluze M. , Fischer J. , González-Alfonso E. , Hurley P. , Lebouteiller V. , Oliver S. J. , Rowan-Robinson M. , Sturm E.
Published: October 2013

We present Herschel photometry and spectroscopy, carried out as part of the Herschel ultraluminous infrared galaxy (ULIRG) survey, and a model for the infrared to submillimetre emission of the ULIRG IRAS 08572+3915. This source shows one of the deepest known silicate absorption features and no polycyclic aromatic hydrocarbon emission. The model suggests that this object is powered by an active galactic nucleus (AGN) with a fairly smooth torus viewed almost edge-on and a very young starburst. According to our model, the AGN contributes about 90 per cent of the total luminosity of 1.1 × 1013 L⊙, which is about a factor of 5 higher than previous estimates. The large correction of the luminosity is due to the anisotropy of the emission of the best-fitting torus. Similar corrections may be necessary for other local and high-z analogues. This correction implies that IRAS 08572+3915 at a redshift of 0.058 35 may be the nearest hyperluminous infrared galaxy and probably the most luminous infrared galaxy in the local (z < 0.2) Universe. IRAS 08572+3915 shows a low ratio of [C ii] to IR luminosity (log L[Cii]/LIR < −3.8) and a [O i]63 μm to [C ii]158 μm line ratio of about 1 that supports the model presented in this Letter.
Proposed Methodology for Quality Preselection of Rice Populations
Authors: Moreira Adriane M. , Bassinello Priscila Z. , Caliari Márcio , Borba Tereza C. O.
Published: October 2013

The evaluation of culinary and sensory characteristics of a particular cultivar is an important trait for rice grain quality because it guides decisions for breeding programs and allows the prediction of rice market acceptance. The aim of this study was to apply direct and indirect tests for the characterization of the grain quality in a segregating rice population under different treatments (2 × 2). A methodology was proposed from the data based on mathematical equations to aid rice breeding programs in the preselection of promising genotypes. Grain samples were evaluated for apparent amylose content, gelatinization temperature, and viscoamylographic profile. In addition, the samples were subjected to a cooking test. The evaluated parameters were weighted and grouped into two linear equations, yielding scores that were subjected to the selection criteria. Using this methodology, families of the studied population were preselected, which reduced the number of samples for final selection by at least 76%. The physical‐chemical analysis did not indicate a direct positive correlation to accurately infer the culinary and sensorial quality of the rice for human consumption, but this analysis was shown to be useful in the preselection of lineages through the proposed strategy.
Methods to Study PAMP-Triggered Immunity in Brassica Species
Authors: Lloyd Simon R. , Schoonbeek Henk-jan , Trick Martin , Zipfel Cyril , Ridout Christopher J.
Published: October 2013

The first layer of active defense in plants is based on the perception of pathogen-associated molecular patterns (PAMPs) leading to PAMP-triggered immunity (PTI). PTI is increasingly being investigated in crop plants, where it may have potential to provide durable disease resistance in the field. Limiting this work, however, is an absence of reliable bioassays to investigate PAMP responses in some species. Here, we present a series of methods to investigate PTI in Brassica napus. The assays allow measuring early responses such as the oxidative burst, mitogen-activated protein kinase phosphorylation, and PAMP-induced marker gene expression. Illumina-based RNA sequencing analysis produced a genome-wide survey of transcriptional changes upon PAMP treatment seen in both the A and C genomes of the allotetraploid B. napus. Later responses characterized include callose deposition and lignification at the cell wall, seedling growth inhibition, and PAMP-induced resistance to Pseudomonas syringae and Botrytis cinerea. Furthermore, using these assays, we demonstrated substantial variation in PAMP responses within a collection of diverse B. napus cultivars. The assays reported here could have widespread application in B. napus breeding and mapping programs to improve selection for broad-spectrum disease resistance.
Sensitivity of Nonexposed and Exposed Populations of Magnaporthe oryzae from Rice to Tricyclazole and Azoxystrobin
Authors: Kunova Andrea , Pizzatti Cristina , Bonaldi Maria , Cortesi Paolo
Published: October 2013

Magnaporthe oryzae is the major pathogen of cultivated rice worldwide, which can cause substantial losses to rice production. Rice blast management is based predominantly on the application of fungicides; however, only a little is known about responses of pathogen populations to the most widely used fungicides. In this work, the baseline sensitivity of the Italian M. oryzae population to tricyclazole and azoxystrobin in terms of mycelium growth was determined, and the possible adaptation of the pathogen population after several years of repeated exposure to fungicide treatments was evaluated. All the analyzed strains demonstrated higher sensitivity and variability to azoxystrobin (concentration of fungicide causing 50% growth inhibition [ED50] = 0.063 mg liter–1) than to tricyclazole (99.289 mg liter–1). After comparing two additional populations collected from fields repeatedly treated with fungicides to the baseline, no decrease in sensitivity toward these fungicides was observed and no resistant strains were detected. The shift of the pathogen sensitivity toward these fungicides has not occurred, although we observed slightly increased variance associated with ED50 of azoxystrobin. Therefore, both azoxystrobin and tricyclazole can be used to manage rice blast in Italy but it will be important to continue monitoring M. oryzae population to early detect possible azoxystrobin resistance.
First Report of Acidovorax avenae subsp. avenae Causing Sugarcane Red Stripe in Gabon
Authors: Girard J.-C. , Noëll J. , Larbre F. , Roumagnac P. , Rott P.
Published: October 2013

During a disease inspection at the sugarcane estate SUCAF near Franceville, Gabon, in March 2011, 1- to 3-mm wide and several dm long dark red stripes were observed on sugarcane (Saccharum spp.) leaves of many plants of cultivar R570. These plants were 5.5 months old in the first ratoon crop. Additionally, spindle leaves of several stalks were rotted and could be easily pulled out of the top of the stalk. Longitudinal sections of diseased stalks showed reddish-brown discoloration of the upper stem and the rotted spindle had an unpleasant odor. Circular, convex, smooth, yellow-cream pigmented bacterial colonies with 2 to 3 mm diameter were isolated after 3 days at 28°C from young leaf lesions on YPGA (yeast extract 7 g/L, peptone 7 g/L, glucose 7 g/L, agar 15 g/L, pH 6.8 to 7.0). The 16S-23S internal transcribed spacer (ITS) of two representative colonies was PCR amplified, and the nucleotide sequences were shown to be 99% identical to the 16S-23S ITS sequence from the genome of Acidovorax avenae subsp. avenae strain ATCC 19860 (GenBank: CP002521.1). One of these A. avenae subsp. avenae isolates from Gabon was inoculated into greenhouse grown plants of sugarcane cultivar R570. Plants were inoculated by injection into the sheath of spindle leaves above the meristem with the bacterial strain (12 plants) or with a water control (six plants). In this method, the bacteria (108 CFU/ml) were injected using a syringe through the leaf sheath until filling the leaf whorl. Three weeks post-inoculation, one to several cm long red-brown stripes were observed on leaves of 11 of 12 inoculated plants. Seven weeks post-inoculation, all plants exhibited symptoms, from red, brown, or black stripes to leaf necrosis, rotting, and death of the spindle leaves (six plants). All six control plants were symptomless. In a second experiment, 6 of 12 plants showed symptoms 3 weeks post inoculation, and the pathogen was successfully re-isolated from all six symptomatic plants with YPGA medium. The 16S-23S ITS of three single colonies obtained each from different symptomatic plants were PCR amplified and the nucleotide sequences were again found 99% identical to the 16S-23S ITS sequence from the genome of A. avenae subsp. avenae ATCC 19860. To our knowledge, this is the first report of A. avenae subsp. avenae, the causal agent of sugarcane red stripe (also reported as top rot), in Gabon. It is also the first description of the occurrence of the top rot form of the disease in R570, a cultivar that is grown in several locations of Africa, the Mascarene Islands, and the French West Indies. A large-scale survey needs to be undertaken to determine the distribution of red stripe in Gabon, a disease for which several outbreaks have been reported recently worldwide (1,2).

References: (1) M. P. Grisham and R. M. Johnson. Phytopathology 101:564, 2011. (2) S. Zia-ul-Hussnain et al. Afr. J. Biotechnol. 10:7191, 2011.
Isoflurane-induced Apoptosis of Neurons and Oligodendrocytes in the Fetal Rhesus Macaque Brain
Authors: Creeley Catherine E. , Dikranian Krikor T. , Dissen Gregory A. , Back Stephen A. , Olney John W. , Brambrink Ansgar M.
Published: October 2013

Background:

The authors have previously shown that exposure of the neonatal nonhuman primate (NHP) brain to isoflurane for 5 h causes widespread acute apoptotic degeneration of neurons and oligodendrocyte. The current study explored the potential apoptogenic action of isoflurane in the fetal NHP brain.

Methods:

Fetal rhesus macaques at gestational age of 120 days (G120) were exposed in utero for 5 h to isoflurane anesthesia (n = 5) or to no anesthesia (control condition; n = 4), and all regions of the brain were systematically evaluated 3 h later for evidence of apoptotic degeneration of neurons or glia.

Results:

Exposure of the G120 fetal NHP brain to isoflurane caused a significant increase in apoptosis of neurons and of oligodendrocytes at a stage when oligodendrocytes were just beginning to myelinate axons. The neuroapoptosis response was most prominent in the cerebellum, caudate, putamen, amygdala, and several cerebrocortical regions. Oligodendrocyte apoptosis was diffusely distributed over many white matter regions. The total number of apoptotic profiles (neurons + oligodendrocytes) in the isoflurane-exposed brains was increased 4.1-fold, compared with the brains from drug-naive controls. The total number of oligodendrocytes deleted by isoflurane was higher than the number of neurons deleted.

Conclusions:

Isoflurane anesthesia for 5 h causes death of neurons and oligodendrocytes in the G120 fetal NHP brain. In the fetal brain, as the authors previously found in the neonatal NHP brain, oligodendrocytes become vulnerable when they are just achieving myelination competence. The neurotoxic potential of isoflurane increases between the third trimester (G120) and the neonatal period in the NHP brain.
Postoperative Changes in Sleep-disordered Breathing and Sleep Architecture in Patients with Obstructive Sleep Apnea
Authors: Chung Frances , Liao Pu , Yegneswaran Balaji , Shapiro Colin M. , Kang Weimin
Published: October 2013

Background:

Anesthetics, analgesics, and surgery may profoundly affect sleep architecture and aggravate sleep-related breathing disturbances. The authors hypothesized that patients with preoperative polysomnographic evidence of obstructive sleep apnea (OSA) would experience greater changes in these parameters than patients without OSA.

Methods:

After obtaining approvals from the Institutional Review Boards, consented patients underwent portable polysomnography preoperatively and on postoperative nights (N) 1, 3, 5, and 7 at home or in hospital. The primary and secondary outcome measurements were polysomnographic parameters of sleep-disordered breathing and sleep architecture.

Results:

Of the 58 patients completed the study, 38 patients had OSA (apnea hypopnea index [AHI] >5) with median preoperative AHI of 18 events per hour and 20 non-OSA patients had median preoperative AHI of 2. AHI was increased after surgery in both OSA and non-OSA patients (P < 0.05), with peak increase on postoperative N3 (OSA vs. non-OSA, 29 [14, 57] vs. 8 [2, 18], median [25th, 75th percentile], P < 0.05). Hypopnea index accounted for 72% of the postoperative increase in AHI. The central apnea index was low (median = 0) but was significantly increased on postoperative N1 in only non-OSA patients. Sleep efficiency, rapid eye movement sleep, and slow-wave sleep were decreased on N1 in both groups, with gradual recovery.

Conclusions:

Postoperatively, sleep architecture was disturbed and AHI was increased in both OSA and non-OSA patients. Although the disturbances in sleep architecture were greatest on postoperative N1, breathing disturbances during sleep were greatest on postoperative N3.
Factors Associated with Postoperative Exacerbation of Sleep-disordered Breathing
Authors: Chung Frances , Liao Pu , Elsaid Hisham , Shapiro Colin M. , Kang Weimin
Published: October 2013

Introduction:

The knowledge on the mechanism of the postoperative exacerbation of sleep-disordered breathing may direct the perioperative management of patients with obstructive sleep apnea. The objective of this study is to investigate the factors associated with postoperative severity of sleep-disordered breathing.

Methods:

After obtaining approvals from Institutional Review Boards, consenting patients underwent portable polysomnography preoperatively, and on postoperative nights 1 and 3 in hospital or at home. The primary outcomes were polysomnography parameters measuring the sleep-disordered breathing. They were treated as repeated measurement variables and analyzed for associated factors by mixed models.

Results:

Three hundred seventy-six patients, 168 men and 208 women, completed polysomnography on preoperative and postoperative night 1. Age was 59 ± 12 yr (mean ± SD). Preoperative apnea–hypopnea index (AHI) was 12 (4, 26) (median [25th, 75th percentile]) events per hour. Thirty-five patients had minor surgeries, 292 intermediate surgeries, and 49 major surgeries, with 210 general anesthesia and 166 regional anesthesia. The 72-h opioid dose was 55 (14, 85) mg intravenous morphine-equivalent dose. Preoperative AHI, age, and 72-h opioid dose were associated with postoperative AHI. Preoperative central apnea index, male sex, and general anesthesia were associated with postoperative central apnea index. Slow wave sleep percentage was inversely associated with postoperative AHI and central apnea index.

Conclusions:

Patients with a higher preoperative AHI were predicted to have a higher postoperative AHI. Preoperative AHI, age, and 72-h opioid dose were positively associated with postoperative AHI. Preoperative central apnea, male sex, and general anesthesia were associated with postoperative central apnea index.
Dietary Fiber Mixture in Pediatric Patients With Controlled Chronic Constipation
Authors: Weber Thabata K. , Toporovski Mauro S. , Tahan Soraia , Neufeld Clarice B. , de Morais Mauro B.
Published: October 2013

Objectives:

The aim of the study was to test the clinical efficacy and effect on colonic transit time (CTT) of a dietary fiber mixture given to children with controlled chronic constipation (CC) after the withdrawal of stool softeners and enemas.

Methods:

This randomized, placebo‐controlled, double‐blind clinical trial involved 54 patients aged 4 to 12 years and had CC that was controlled by the use of low‐dose stool softeners. The use of these softeners was discontinued when the patients were admitted to the clinical trial. The patients were randomized into 2 groups for the 4‐week study period. One group received a dietary fiber mixture and the other group received a placebo (maltodextrin). The primary outcome was therapeutic failure (oral stool softeners or enemas was required to prescribe during the trial). Secondary outcomes included defecation frequency, stool consistency (measured using the Bristol Stool Form Scale), and CTT.

Results:

Therapeutic failure was observed in 34.6% (9/26) of the patients in the dietary fiber mixture group and in 35.7% (10/28) in the control group (P = 0.933). The mean increase in daily bowel movements was 0.53 in the dietary fiber mixture group and 0.23 in the control group (P = 0.014). The patients in the dietary fiber mixture group (60.0%) passed nonhardened stools more frequently than did those in the control group (16.7%, P = 0.003). The CTT was similar for both groups.

Conclusions:

The fiber mixture did not prevent the suspension of stool softeners or lead to reduced CTT; however, the mixture promoted an increased frequency of defecation and an improvement in the stool consistency.
The role of serious concomitant injuries in the treatment and outcome of pediatric severe traumatic brain injury
Authors: Stewart Tanya Charyk , Alharfi Ibrahim M. , Fraser Douglas D.
Published: October 2013

BACKGROUND

The study objective was to describe the epidemiology of serious concomitant injuries and their effects on outcome in pediatric severe traumatic brain injury (sTBI).

METHODS

A retrospective cohort of all severely injured (Injury Severity Score [ISS] ≥ 12) pediatric patients (<18 years) admitted to our pediatric intensive care unit, between 2000 and 2011, after experiencing an sTBI (Glasgow Coma Scale [GCS] score ≤ 8 and head Abbreviated Injury Scale [AIS] ≥ 4) were included. Two groups were compared based on the presence of serious concomitant injuries (maximum AIS score ≥ 3). Multivariate logistic regression was undertaken to determine variable associations with mortality.

RESULTS

Of the 180 patients with sTBI, 113 (63%) sustained serious concomitant injuries. Chest was the most commonly injured extracranial body region (84%), with lung being the most often injured. Patients with serious concomitant injuries had increased age, weight, and injury severity (p < 0.001) and were more likely injured in a motor vehicle collision (91% vs. 48%, p < 0.001). Those with serious concomitant injuries had worse sTBI, based on lower presedation GCS (p = 0.031), higher frequency of fixed pupils (p = 0.006), and increased imaging abnormalities (SAH and DAI, p ≤ 0.01). Non-neurosurgical operations and blood transfusions were more frequent in the serious concomitant injury group (p < 0.01). The differences in mortality for the two groups failed to reach statistical significant (p = 0.053), but patients with serious concomitant injuries had higher rates of infection and acute central diabetes insipidus, fewer ventilator-free days, and greater length of stays (p < 0.05). Multivariate analyses revealed fixed pupillary response (odd ratio [OR], 63.58; p < 0.001), presedation motor GCS (OR, 0.23; p = 0.001), blood transfusion (OR, 5.80; p = 0.008), and hypotension (OR, 4.82; p = 0.025) were associated with mortality, but serious concomitant injuries was not (p = 0.283).

CONCLUSION

Head injury is the most important prognostic factor in mortality for sTBI pediatric patients, but the presence of serious concomitant injuries does contribute to greater morbidity, including longer stays, more infections, fewer ventilator-free days, and a higher level of care required on discharge from hospital.

LEVEL OF EVIDENCE

Prognostic and epidemiologic study, level III.